Warnock, Yang and Donoghue: Supplementary Information
Literature survey
To investigate the present trend for representing palaeontological data in Bayesian molecular clock analysis, we
undertook a review of studies published within the past year. Publications included in this survey were selected
through the ISI Web of Science using the following search criteria:
-
Studies published between January 2010 and April 2011 and citing the relaxed clock model
implemented in BEAST [1]. BEAST is presently the most popular software package for the Bayesian
estimation of divergence times and offers a wide range of probability distributions to constrain node
ages.
-
Included the term “molecular clock” either in the title, key words or abstract, thus refining our search to
studies whose primary goals included molecular dating.
We excluded the following:
-
Studies that did not perform any molecular analysis using BEAST
-
Publications that did not feature any geological or palaeontological based calibrations (e.g. those that
applied an average substitution rate obtained elsewhere or used simulated data)
-
Molecular clock analysis that calibrated trees using non-zero terminals
This resulted in a total of 39 publications from which we documented the variable approaches to calibrating the
molecular clock. When multiple molecular clock methods were included in the materials and methods, we report
only the calibrations that apply to the BEAST analysis.
Table 1: Literature Review on the nature of fossil based calibrations employed in Bayesian molecular clock analyses, 2010-2011
Evidencee
Reference
Allwood et al 2010 [2]
Bouetard et al 2010 [3]
Brandley et al 2010 [4]
Brown et al 2010 [5]
Colangelo et al 2010 [6]
Couvreur et al 2010 [7]
Crisp et al 2010 [8]
Datzmann et al 2010 [9]
de Thoisy et al 2010 [10]
Dentinger et al 2010 [11]
Derkarabetian et al 2010
[12]
Dinapoli & KlussmannKolb 2010 [13]
Edwards & Melville 2010
[14]
Fulton & Strobeck 2010
[15]
Göbbeler & KlussmannKolb 2010 [16]
Gustafsson et al 2010 [17]
He et al 2010 [18]
Hoffmann et al 2010 [19]
Jörger et al 2010 [20]
Light et al 2010 [21]
Liu et al 2010 [22]
Magallón 2010 [23]
Meredith et al 2010a [24]
Meredith et al 2010b [25]
Muellner et al 2010 [26]
Olson et al 2010 [27]
Päckert et al 2010 [28]
Papadopoulou et al 2010
[29]
Perini et al 2010 [30]
Pons et al 2010 [31]
Renner & Schaefer 2010
[32]
San Mauro 2010 [33]
Schaefer & Renner 2010
[34]
Silberfeld et al 2010 [35]
Smith et al 2010 [36]
Ward et al 2010 [37]
Davy et al 2011 [38]
Melville et al 2011 [39]
Simonsen et al 2011 [40]
Calibration
densityd
Justifiedf
Distributiong
Primary
Secondary
Total no.
Calibrationsa
Calibrationsb
calibrationsc
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
1
1 (Alt)
3
1
5
1
3 (Alt)
3
2
1 (Alt)
27
76
20.67
89
7.6
235
17.33
14.33
27
28
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
-
yes
yes
yes
yes
yes
yes
yes
yes
yes
-
yes
yes
-
yes: N (Alt)
yes: N
yes: LN
yes: N (Alt)
yes: N, LN
yes: N
yes: LN, N
yes: E, LN
yes: N
yes: N
yes
none
none
none
none
yes
none
none
none
yes
yes
-
3
18.33
yes
yes
yes
yes
-
yes: LN, G, N
yes
yes
-
3
17.33
yes
-
yes
-
-
yes: N
yes
yes
-
5
13.2
yes
yes
yes
-
-
yes: LN, N
none
yes
-
8 (Alt)
3.63
yes
-
yes
yes
-
yes: LN, G, N
yes
yes
yes
yes
yes
yes (host)
yes
yes
yes
yes
yes (host)
yes
yes
yes
yes
yes
-
2
4 (Alt)
3
2
3
3
6 (Alt)
21
1
9
3
1
1
18
17.5
15
97
26
24
6.67
3.33
17
2.44
8
84
15
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
-
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
yes
-
yes
yes
yes
yes
-
yes
NA
yes
yes
yes
yes: N
yes: N
yes: LN
NA
yes: G
yes: N
yes: E
yes: LN
yes: N
yes: N (Alt)
yes: N
yes: E
-
none
none
yes
none
yes
yes
none
none
none
none
none
yes
none
yes
yes
yes
-
6
3
1
10
9.67
13
yes
yes
yes
-
yes
yes
yes
-
-
yes: N
yes: G
yes: N
none
none
none
yes
yes
yes
-
7
5 (Alt)
89.43
5.2
yes
yes
-
yes
yes
yes
-
yes: N
yes: LN
none
none
yes
yes
yes
yes
yes
yes
yes
yes
yes
-
5
4
33
7
2
6
3
13
18
4.67
7.71
24.5
NA
11.67
yes
yes
yes
yes
yes
yes
-
yes
yes
yes
yes
yes
yes
-
yes
NA
-
yes: LN
yes: N
yes: LN
yes: LN
NA
yes: LN, N
yes: LN, N
none
yes
yes
none
none
none
none
Fossil
Bio –/palaeogeographic
Minimum
Maximum
Uniform
Non-uniform
Justificationh
a
Primary calibrations are based directly on primary palaeontological evidence. ‘Host’ indicates that the fossil
record of a host species was used to infer calibrations
b
Secondary calibrations are derived from previously published molecular clock estimates, regardless of the
method used to obtain these dates
c
Total number of calibrations, includes both ingroup and outgroup calibrations and refers to the maximum
number of nodes calibrated in any single analysis. ‘Alt’ indicates that the study experimented with alternative
calibrations for comparison
d
Calibration density is measured as the number of terminals per calibration
e
Evidence indicates whether the calibrations were obtained from fossil or geographic evidence
f
Justified minima and maxima refers to any description of where the minimum and/or maximum dates were
obtained based on primary fossil based evidence; this includes references to other publications.
g
Non-uniform distributions: E = exponential, G = gamma, LN = lognormal, N = normal. Where “Alt” is
indicated, non-uniform distributions have been used in an alternative analysis for comparison
h
Justification indicates any justification of the use of a given distribution however vague, including references to
other publications
NA indicates relevant information was not provided
Materials and methods
Taxon sampling and molecular markers
There are a total of 66 arthropods listed on the NCBI Entrez Genome Project database, 2 complete, 37 draft
assembly stage and 27 in progress. We chose representatives of the 15 families that have reached draft assembly
stage - Acyrthosiphon pisum, Anopheles gambiae, Apis mellifera, Bombyx mori, Camponotus floridanus,
Daphnia pulex, Drosophila melanogaster, Ixodes scapularis, Lepeophtheirus salmonis, Mayetiola destructor,
Nasonia vitripennis, Pediculus humanus, Rhodnius prolixus, Tribolium castaneum and Varroa destructor. We
assembled a matrix of amino acid for seven nuclear housekeeping genes that have been used previously to
estimate divergence times among metazoans [41], aldolase (ALD), ATP synthase  chain (ATPB), catalase
(CAT), elongation factor 1- (EF1), methionine adenosyltransferase (MAT), phosphofructokinase (PFK), and
triosephosphate isomerase (TPI). When protein sequences could not be directly retrieved from the RefSeq or
Non-RefSeq protein databases, exon sequences were predicted from whole genome shotgun sequences using
TBLASTN [42] and GenScan [43].
Topology
We employed a fixed consensus topology throughout our analyses based on recent comprehensive studies [44,
45].
Alignment and model selection
Sequences were aligned using MUSCLE [46] with further manual alignment. Regions that could not be
unambiguously aligned were removed. Individual protein alignments were concatenated and treated as a single
partition. The final alignment contained 2316 characters, including 7.8% missing data an d gaps. The optimum
substitution model and among-site rate heterogeneity parameters were selected using the Bayesian information
criterion in the program Prottest [47], with five gamma rate categories and excluding models that cannot be
implemented in both BEAST and MCMCTREE. WAG +  was estimated as the best-fit model.
Molecular clock analysis
The independent rate-drift model was used to estimate divergence times in BEAST [1] and MCMCTREE [48],
with a gamma distribution applied to the overall substitution rate, ucld.mean in BEAST and rgene_gamma in
MCMCTREE, with mean and standard deviation G(0.03, 0.03). The prior used to describe how variable rates are
across branches specified as G(0.316, 0.316) in BEAST (ucld.stdev) and G(0.1, 0.1) in MCMCTREE
(sigma2_gamma). It should be noted that the mean and standard deviation are specified differently in BEAST
and MCMCTREE; mean =  and m =/, respectively. Because we used fossil evidence to constrain all 14
nodes, the speciation models do not apply here. The ultrametric tree generated in MCMCTREE was using as the
starting tree in BEAST.
The approximate likelihood calculation was used to estimate divergence times in MCMCTREE, with maximum
likelihood estimates of branch lengths calculated in CODEML, using the WAG + 5 model. In MCMCTREE,
we ran two independent chains each consisting of 5 million iterations, discarding the first 0.5 M generations as
burn-in and sampling every 100 generations, resulting in a total of 45,000 samples post burn-in. In BEAST we
ran two independent chains each consisting of 10 million iterations, 3 M generations burn-in and sampling every
100, resulting in 70,000 samples. All MCMC output was visualized in Tracer 1.5 [1].
Calibrations:
1. Euarthropoda: Ixodes, Varroa – copepod, Daphnia, louse, aphid, Rhodnius, Nasonia, ant, bee, beetle,
silkmoth, mosquito, fruitfly, Mayetiola (515 Ma; soft max 636.1 Ma)
This represents the divergence of Mandibulata from Chelicerata. The earliest possible evidence of arthropods is
Rusophycus-like trace fossils from the Upper Nemakit-Daldynian of Mongolia [49, 50]. The Nemakit-Daldynian
– Tommotian has recently been dated at 524.837 ± 0.092 [51]. Rusophycus tracefossils are invariably attributed
to trilobites. However, the certainty of the link to trilobites is not sufficient to justify a minimum constraint, not
least since these traces are merely Rusophycus-like. And although trilobites are considered by some stemCherlicerata [52, 53] and, therefore, crown-Arthropoda, the certainty with which trilobites can be assigned to
crown-Arthropoda remains open to question [54]. The oldest undisputed arthropods are the crown-crustaceans
Yicaris dianensis [55] and Wujicaris muelleri [56], both of which were recovered from strata belonging to the
Eoredlichia – Wutingaspis Biozone. Chinese Cambrian stratigraphy has been revised substantially and the
Eoredlichia – Wutingaspis Biozone is no longer recognized [57, 58]. However, Eoredilichia is known to cooccur with Hupeidiscus which is diagnostic of the Hupeidiscus-Sinodiscus Biozone which is formally recognised
as the second biozone of the Nangaoan Stage of the Qiandongian Series of the Cambrian of China. The
Nangaoan is the proposed third stage of the Cambrian System for the International Geologic Timescale. Thus, a
minimum constraint on the age of Yicaris dianensis and Wujicaris muelleri, the oldest certain records of crownArthropoda, can be derived from the top of the Nangaoan which has been dated to 515 Ma [59].
A soft maximum constraint is based on the maximum age interpretation of the Lantian Biota [60]. This, together
with the Doushantuo Biota [61] provide a series of Lagerstatten preserving the biota in Orsten- and Burgess
Shale-like modes of fossilization. None of these Lagerstatten, least of all the Lantian preserve anything that
could possibly be interpreted as even a total group arthropod and on this basis we define out soft maximum
constraint at 635.5 ± 0.6 Ma [62] and, thus, 636.1 Ma.
2. Parasitiformes: Ixodes – Varroa (min: 91.1 Ma; soft max: 636.1 Ma)
This is the principal divergence within crown-Parasitiformes, between Ixodes scapularis (Ixodiida) and Varroa
destructor (Mesostigmata). The oldest record of Mesostigmata is represented a phytoseiid from Eocene Baltic
amber [63]; there are much older records of Ixodiida. The oldest possible records of Ixodiida is from Burmese
Amber the dating evidence is insubstantial [64] or else it has not been substantiated [65]. The next oldest record
is Carios jerseyi from late Cretaceous New Jersey Amber at Sayreville [66] where, according to Michener &
Grimaldi [67] the amber occurs within the Woodbridge Clay Member of the Raritan Formation, palynological
zone IV [sensu 68]. This is equivalent to Calcareous Nannofossil Zones CC10 and CC11 which span the upper
Cenomanian to lower and middle Turonian age [69]. In the absence of additional constraints it is possible to
derive a minimum constraint on date of the end of CC11, thus, 91.1 Ma [70].
A soft maximum constraint is based on the maximum age interpretation of the Lantian Biota [60]. This, together
with the Doushantuo Biota [61] provide a series of Lagerstatten preserving the biota in Orsten- and Burgess
Shale-like modes of fossilization. None of these Lagerstatten, least of all the Lantian preserve anything that
could possibly be interpreted as even a total group arthropod and on this basis we define out soft maximum
constraint at 635.5 ± 0.6 Ma [62] and, thus, 636.1 Ma.
3. Mandibulata: Daphnia, copepod – louse, Rhodnius, aphid, Nasonia, ant, honeybee, beetle, silkmoth,
mosquito, fruitfly, Mayetiola (min: 515 Ma; soft max 543 Ma)
This represents the establishment of crown Mandibulata and the divergence of Crustacea from Hexapoda. The
earliest possible crustaceans have been reported from the Mount Cap Formation of northwestern Canada [71].
However, these remains are fragmentary and their interpretation as crustaceans is based on the special similarity
between between individual fragments and the filter feeding apparatus of modern branchiopod crustaceans,
rather than on the basis of a suite of mutually corroborative phylogenetically informative characters. The earliest
convincing evidence for the divergence of Crustacea and Hexapoda are the crown-crustaceans Yicaris dianensis
[55] and Wujicaris muelleri [56], both of which were recovered from strata belonging to the Eoredlichia –
Wutingaspis Biozone. Chinese Cambrian stratigraphy has been revised substantially and the Eoredlichia –
Wutingaspis Biozone is no longer recognized [57, 58]. However, Eoredilichia is known to co-occur with
Hupeidiscus which is diagnostic of the Hupeidiscus-Sinodiscus Biozone which is formally recognised as the
second biozone of the Nangaoan Stage of the Qiandongian Series of the Cambrian of China. The Nangaoan is
the proposed third stage of the Cambrian System for the International Geologic Timescale. Thus, a minimum
constraint on the age of Yicaris dianensis and Wujicaris muelleri, the oldest certain records of crownArthropoda, can be derived from the top of the Nangaoan which has been dated to 515 Ma [59].
A soft maximum constraint may be provided by the earliest evidence of arthropods, based upon
Ruzophycus-like tracefossils from the Nemakit-Daldynian (early Tommotian) of Mongolia (400, 401)[49, 72]. A
soft maximum constraint may therefore be derived from the base of the Nemakit-Daldynian which equates to the
base of the Cambrian and, thus, 542 Ma ± 1.0 myr [73]. Our soft maximum constraint is therefore 543 Ma.
4. Daphnia – copepod (min: 499.0; soft max: 543 Ma)
This represents the divergence of Branchiopoda and Copepoda within Crustacea. Unfortunately, the internal
relationships within Crustacea are in a state of flux [74]. In the last year, Branchiopoda and Copepoda have been
resolved as immediate sister taxa [75], comprising a clade but intercalated by Malacostraca and Thecostraca
[44], and Branchiopoda has been resolved as more closely related to Hexapoda than to Copepoda [45]. Since that
debate is so far from consensus it is necessary to take the most conservative approach to establishing a minimum
constraint, by identifying the oldest record of the total group Copepoda and total group Branchiopoda.
Copepods have an appalling fossil record but the oldest possible record is based on fragmentary remains from
the latest Carboniferous [76]. Regardless of these veracity of this record, it is considerably younger than the
oldest records of Branchiopoda. The oldest possible branchiopod is based on fragmentary remains from the
Early Cambrian [71], however, though these fossil fragments are exquisitely preserved, they lack sufficient
anatomical data to corroborate the comparison to branchiopods that character congruence would afford.
Alternatively, the ontogeny of the Late Cambrian Rehbachiella has been described from the first to the last instar
based on three dimensional soft tissue remains from the Orsten Lagerstatte of Sweden [77-79]. The Orsten
deposit falls within the Agnostic pisiformis Biozone which is the last within the Guzhangian [80] and so a
minimum age can be derived from the base of the overlying Paibian Stage and Furongian System, 499.0 Ma
[59].
A soft maximum constraint may be provided by the earliest evidence of arthropods, based upon
Ruzophycus-like tracefossils from the Nemakit-Daldynian (early Tommotian) of Mongolia (400, 401)[49, 72]. A
soft maximum constraint may therefore be derived from the base of the Nemakit-Daldynian which equates to the
base of the Cambrian and, thus, 542 Ma ± 1.0 myr [73]. Our soft maximum constraint is therefore 543 Ma.
5. Eumetabola: louse, Rhodnius, aphid - Nasonia, ant, honeybee, beetle, silkmoth, mosquito, Drosophila,
Mayetiola (min 307.2 Ma; soft max 414 Ma)
The divergence of Paraneoptera from Holometabola. Providing a minimum constraint on the divergence of
crown-Eumetabola is complicated by the lack of resolution concerning the affinity of Palaeodictyopterida which
has been variably considered a member of the clade. Grimaldi and Engel exclude palaeodictyopterids from the
clade leaving Miomoptera as the oldest members of Eumetabola [81]. These authors discuss the various possible
affinities of Mimptera among Paraneoptera or Holometabola, but there appears no equivocation of their
membership of Eumetabola. The oldest known record of Miomoptera is an undescribed specimen (Field
Museum PE 293590 from the Pennsylvanian Mazon Creek Lagerstatte [82]). The Mazon Creek fauna is derived
from the Francis Creek Member of the Carbondale Formation in NE Illinois. The Francis Creek Shale Member
has been dated as middle Desmoinesian and middle Westphalian D age on the basis of both palynological and
paleobotanical data [83-85]. This equates to the upper part of the Moscovian Stage, the top of which has been
dated at 306.5 Ma ± 1.0 myr on the basis of a graphically-correlated composite standard calibrated using
radiometric dates [86]. The top of the Westphalian D is slightly older at 307.2 Ma [86]. Thus, the minimum
constraint on the divergence of crown-Eumetabola is 305.5 Ma.
A soft maximum constraint may be provided by the age of the oldest insect Rhyniognatha hirtsi from
the Early Devonian Rhynie Chert of northeast Scotland [87]. The age of the Rhynie Chert has been best
established on the basis of the composition of its spore assemblages which indicate an early Pragian to ?earliest
Emsian age span [88]. Thus, we may establish a soft maximum constraint on the base of the Pragian which is
411.2 Ma ± 2.8 myr [89], equating to 414 Ma.
6. Paraneoptera: Louse – Rhodnius, Aphid (min 283.7 Ma; soft max 414 Ma)
Though the assignment of Archescytinidae to the hemipteran crown group may be questioned, there is no
question of its membership of Paraneoptera. There are older records of Paraneoptera, including Permopsocidae,
but these are likely stem-Paraneoptera [81, 90]. Thus, the best minimum constraint on the divergence of
Paraneoptera is provided by an undescribed archescytinid from the Middle Bacov Beds of Boscovice Furrow,
Obora Czech Republic [91, 92]. These rocks were described as Artinskian by Kucklova-Peck and Willman [92],
without justification, but they have subsequently been attributed to the Sakmarian using vertebrate microremians
for biostratigraphic correlation [93, 94]. On this basis we may use the top of the Sakmarian as our basis for a
minimum constraint on the divergence of Paraneoptera and Holometabola which is as given as 284.4 ± 0.7 myr
[95], providing the minimum constraint of 283.7 Ma.
The most approximate soft maximum constraint on the divergence of Paraneoptera is provided by the
earliest records of Neoptera, which are a paraphyletic assemblage of late Carboniferous roach-like dictyopterans,
sometimes grouped as the grade Blattodea or Blatoptera. The oldest such record is probably Ctenopilus
elongatus (previously Eoblattina complexa) from the Stephanian B-C of the Commentary Basin, France [96].
The Stephanian B of western Europe correlates to the upper Kasimovian of the 2004 Geologic Timescale, the
base of which has been dated at 306.5 Ma ± 1.0 myr [86] and, thus, a soft maximum constraint of 307.5 Ma.
However, given the reliance on temporally isolated lagerstatte for constraining the temporal diversification of
insects, this envelope is perhaps too strict. Instead, a more appropriate soft maximum constraint may be provided
by the oldest member of Pterygota, the oldest possible record of whch is also the oldest known insect,
Rhyniognatha hirsti [87], providing a constraint of 414 Ma (see Eumetabola above).
7. Hemiptera: Rhodnius – Aphid (min 199.0 Ma; soft max 307.5 Ma)
The oldest known hemipterans are members of the Archescytinidae, the oldest record of which remains
undescribed but has been recorded from the early Artinskian locality of Obora [91]. Archescytinidae is identified
by Shcherbakov and Popov as more closely related to aphids than to Cimicina and, hence, providing a minimum
constraint on the split between Rhodnius and aphids [91]. However, Engel and Grimaldi question this
interpretation of the affinity of Archescytinidae within Hemiptera because the necessary characters are not
preserved. Engel and Grimaldi (p. 321) describe 3 unnamed heteropterans from the Triassic of Virginia (USA),
but the oldest described taxon is Lufengnacta (Corixidae, Nepomorpha, Panheteroptera, Heteroptera) from the
Yipinglang Coal Series of Yunnan Province, China. The age of the Yipinglang Coal Series is widely agreed to
be of Late Triassic age and has been used to justify the correlation of overlying units across South China. Its
precise age may be constrained by the palynoflora [97] which provides a Rhaetian-Norian age. Thus, the
minimum constraint on the divergence of crown Hemiptera is provided by the date for the end Rhaetian (end
Triassic), which is 199.6 Ma ± 0.6 myr [98] and, thus, 199.0 Ma.
A suitable soft maximum constraint may be provided by the earliest Neopteran, which is Ctenopilus
elongatus [96], providing a date of 307.5 Ma (see Paraneoptera above).
8. Endopterygota/Holometabola: Wasp, Ant, Honeybee – Beetle, Silkmoth, Mosquito, Fruitfly, Mayetiola
(min 307.2 Ma; soft max 414 Ma)
Divergence of crown Holometabola/Endopterygota into Hymenoptera and Panorpida. The oldest recorded
member of this clade appears to be an undescribed member of Coleopteroidea from the Middle Carboniferous
Mazon Creek fauna of Illinois, USA [82]. The Mazon Creek fauna is derived from the Francis Creek Member of
the Carbondale Formation in NE Illinois. The Francis Creek Shale Member has been dated as middle
Desmoinesian and middle Westphalian D age on the basis of both palynological and paleobotanical data [83-85].
This equates to the upper part of the Moscovian Stage, the top of which has been dated at 306.5 Ma ± 1.0 myr on
the basis of a graphically-correlated composite standard calibrated using radiometric dates [86]. The top of the
Westphalian D is slightly older at 307.2 Ma [86]. Thus, the minimum date on the divergence of these two clades
is 307.2 Ma.
A soft maximum constraint may be provided by the age of the oldest insect Rhyniognatha hirtsi from the Early
Devonian Rhynie Chert of northeast Scotland [87]. The age of the Rhynie Chert has been best established on the
basis of the composition of its spore assemblages which indicate an early Pragian to ?earliest Emsian age span
[88]. Thus, we may establish a soft maximum constraint on the base of the Pragian which is 411.2 Ma ± 2.8 myr
[89], equating to 414 Ma.
9. Apocrita: Honeybee, Ant – Wasp (min 152 Ma; soft max 243 Ma)
The divergence of the honeybee Apis from from the parasitic wasp Nasonia corresponds to the crown group
concept of the hymenopteran suborder Apocrita, and the divergence of Proctotrupoidea and Chalcidoidea,
respectively. The oldest records of both lineages are at minimum, late Jurassic in age, but the earliest record of
Proctotrupoidea are the best dated. These earliest records belong to Mesoserphidae, such as Mesoserphus and
Karatoserphus, from the early Jurassic Daohugou Beds of Inner Mongolia, China [99, 100]. The age of these
beds has been constrained radiometrically using U-Pb series dating to the interval 168-152 Ma [101, 102] and,
thus, we take 152 Ma as the minimum constraint on the divergence of honeybee and wasp.
A soft maximum constraint can be provided by the earliest record of Hymentoptera, the earliest
recognized members of which are from the Middle Triassic Madygen Formation of Central Asia [103, 104], that
is dated as Ladinian and/or Carnian on the basis of palynological data [105, 106]. Thus, the constraint may be
derived from the base of the Ladinian, which may be as much as 241 Ma ± 2.0 myr [98], equating to a soft
maximum constraint of 243 Ma.
10. Aculeata: Honeybee – Ant (min 92.7 Ma; soft max 243 Ma)
The oldest possible record of the bee lineage is Melittosphex burmensis, the precise affinity of which has been
disputed [107-109]. The oldest ants are also known from this same deposit [64] which is unfortunate since the
dating evidence is insubstantial [64] or else it has not been substantiated [65]. Definitive members of the ant total
group have been described from the Charente-Maritime of France and have been considered approximate age
equivalents of the Burmese Amber [110, 111]. The age of the amber-bearing deposit has been reported widely
as Albian [112, 113] but the palynological evidence could substantiate an age as young as Cenomanian [114].
The top of the Cenomanian is dated to 93.5 Ma ± 0.8 Myr [70], providing for a minimum constraint on the
divergence of Honeybee and Ant of 92.7 Ma.
A soft maximum constraint can be provided by the earliest record of Hymentoptera, the earliest
recognized members of which are from the Middle Triassic Madygen Formation of Central Asia [103, 104], that
is dated as Ladinian and/or Carnian on the basis of palynological data [105, 106]. Thus, the constraint may be
derived from the base of the Ladinian, which may be as much as 241 Ma ± 2.0 myr [98], equating to a soft
maximum constraint of 243 Ma.
11. Tribolium - Bombyx, Anopheles, Drosophila, Mayetiola (min 307.2 Ma; soft max 414 Ma)
The oldest recorded member of this clade appears to be an undescribed member of Coleopteroidea from the
Middle Carboniferous Mazon Creek fauna of Illinois, USA [82]. The Mazon Creek fauna is derived from the
Francis Creek Member of the Carbondale Formation in NE Illinois. The Francis Creek Shale Member has been
dated as middle Desmoinesian and middle Westphalian D age on the basis of both palynological and
paleobotanical data [83-85]. This equates to the upper part of the Moscovian Stage, the top of which has been
dated at 306.5 Ma ± 1.0 myr on the basis of a graphically-correlated composite standard calibrated using
radiometric dates [86]. The top of the Westphalian D is slightly older at 307.2 Ma [86]. Thus, the minimum date
on the divergence of these two clades is 307.2 Ma.
A soft maximum constraint may be provided by the age of the oldest insect Rhyniognatha hirtsi from the Early
Devonian Rhynie Chert of northeast Scotland [87]. The age of the Rhynie Chert has been best established on the
basis of the composition of its spore assemblages which indicate an early Pragian to ?earliest Emsian age span
[88]. Thus, we may establish a soft maximum constraint on the base of the Pragian which is 411.2 Ma ± 2.8 myr
[89], equating to 414 Ma.
12. Bombyx – Anopheles, Drosophila, Mayetiola (min 238.5 Ma; soft max 295.4 Ma)
This represents the divergence between Amphiesmenoptera (Lepidoptera+Trichoptera) and Diptera. The oldest
records of Lepidoptera and Trichoptera are early Jurassic and, therefore, considerably younger than the oldest
records of Diptera. Though there are candidate stem-Diptera from the Permian their relationships are poorly
understood and so we advocate a minimum constraint based on the oldest records of crown-Diptera, Grauvogelia
arzvillerianai, Gallia alsatica, Vymrhyphus blagoderovi (among others), all from the Triassic Grès-a-Voltzia
Formation of France [115, 116].
The Grès à Meules facies of the Grès-a-Voltzia Formation, from which these remains are derived, has been dated
as Lower Anisian [117, 118], although the evidence on which this is based was not presented. The top of the
Lower Anisian is dated as 240.5 Ma, based on proportional scaling of major conodont zones [98] from a graphic
correlation global composite standard [119], from which an error of ±2.0 myr is derived. Thus, the minimum
date for the divergence of the lineages leading to Anopheles gambiae and Drosophila melanogaster plus
Mayetiola destructor, is 238.5 Ma.
A soft maximum constraint is provided by the insect fauna of Boskovice Furrow, Oboro, Moravia, Czech
Republic. A huge diversity of insects has been described from this deposit which is the single most important
Palaeozoic insect locality in the World [81]. No members of even total group Diptera have been described from
here or from younger deposits. The Oboro fauna has been dated at early Artinskian [92] and Sakmarian [94],
although only the latter has been substantiated. The base of the Sakmarian has been dated at 294.6 Ma ± 0.8 myr
[95]. Thus, the soft maximum constraint on the divergence of Brachycera and Culicomorpha can be taken as
295.4 Ma.
13. Diptera: Anopheles – Drosophila, Mayetiola (min 238.5 Ma; soft max 295.4 Ma)
The veracity of some of the high level rank taxa within Diptera are currently disputed. The long standing
dichotomy between Brachycera and Nematocera has been questioned in recent analyses which recover a
paraphyletic Nematocera in which Mayetiola is more closely related to Drosophila (and a monophyletic
Brachycera) than Anopheles [45]. This is the scheme of relationships in which the interrelationships of fossil taxa
have been considered [81] and this recognizes members of grauvogeliid Psychodomorpha, specifically,
Grauvogelia arzvilleriana from the Triassic Grès-a-Voltzia Formation of France [115]. The oldest documented
representatives of Brachycera are from the Triassic Dan River Group of Virginia [120, 121], although their
assignment rests upon precious few and largely inconsistent venation characters [81]. There remains an older
record of Brachycera, Gallia alsatica, from the Grès-à-Voltzia Formation of Arzviller, northeast France
(recognized on the basis of the following derived characters: cell m3 narrowed distally and Cu and A1
terminating in one point at the wing margin) [121, 122].
The Grès à Meules facies of the Grès-a-Voltzia Formation, from which these remains are derived, has been dated
as Lower Anisian [117, 118], although the evidence on which this is based was not presented. The top of the
Lower Anisian is dated as 240.5 Ma, based on proportional scaling of major conodont zones [98] from a graphic
correlation global composite standard [119], from which an error of ±2.0 myr is derived. Thus, the minimum
date for the divergence of the lineages leading to Anopheles gambiae and Drosophila melanogaster plus
Mayetiola destructor, is 238.5 Ma.
A soft maximum constraint is provided by the insect fauna of Boskovice Furrow, Oboro, Moravia, Czech
Republic. A huge diversity of insects has been described from this deposit which is the single most important
Paleozoic insect locality in the World [81]. No members of Diptera have been described from here or from
younger deposits. The Oboro fauna has been dated at early Artinskian [92] and Sakmarian [94], although only
the latter has been substantiated. The base of the Sakmarian has been dated at 294.6 Ma ± 0.8 myr [86]. Thus,
the soft soft maximum constraint on the divergence of Brachycera and Culicomorpha can be taken as 295.4 Ma.
14. Drosophila – Mayetiola (min 238.5 Ma; soft max 295.4 Ma)
This constitutes the divergence between Brachycera and Cecidomyiidae within the monophyletic rump of
anotherwise paraphyletic Bibionomorpha [81, 116]. The oldest record of Brachycera is Gallia alsatica, from the
Grès-à-Voltzia Formation of Arzviller, northeast France (recognized on the basis of the following derived
characters: cell m3 narrowed distally and Cu and A1 terminating in one point at the wing margin) [121, 122]. The
oldest stem-Brachycera recognized Vymrhyphus blagoderovi is also from the Grès-à-Voltzia Formation of
Arzviller [116, 121]. The Grès à Meules facies of the Grès-a-Voltzia Formation, from which these remains are
derived, has been dated as Lower Anisian [117, 118], although the evidence on which this is based was not
presented. The top of the Lower Anisian is dated as 240.5 Ma, based on proportional scaling of major conodont
zones [98] from a graphic correlation global composite standard [119], from which an error of ±2.0 myr is
derived. Thus, the minimum date for the divergence of the lineages leading to Drosophila melanogaster and
Mayetiola destructor, is 238.5 Ma.
A soft maximum constraint is provided by the insect fauna of Boskovice Furrow, Oboro, Moravia, Czech
Republic. A huge diversity of insects has been described from this deposit which is the single most important
Paleozoic insect locality in the World [81]. No members of Diptera have been described from here or from
younger deposits. The Oboro fauna has been dated at early Artinskian [92] and Sakmarian [94], although only
the latter has been substantiated. The base of the Sakmarian has been dated at 294.6 Ma ± 0.8 myr [95]. Thus,
the soft soft maximum constraint on the divergence of Brachycera and Culicomorpha can be taken as 295.4 Ma.
Table 2: Posterior age estimates (mean and 95% HPD limits) obtained using arbitrary (minima only) and bespoke (minima and maxima) prior calibrations in BEAST and
MCMCtree. Node ID corresponds to those shown Figure 1.
Node
Mean
Lower and upper
ID
95% HPDs
Analysis in BEAST
Lognormal minima only,
s=0.5, m=1
1
2
3
4
5
6
7
8
9
10
11
12
13
14
628
362
619
608
539
474
443
501
280
220
464
429
367
316
613
264
599
582
501
415
376
464
221
164
424
388
328
280
636
457
636
631
574
528
510
541
346
283
504
468
407
357
Analysis in MCMCtree
Cauchy minima only,
p=0.1, c=0.2
1
2
3
4
5
6
7
8
9
10
11
12
13
14
596
346
557
537
436
381
348
393
178
129
358
327
280
247
544
228
515
499
389
316
271
353
152
96
322
295
257
239
Mean
Lower and upper
95% HPDs
Lower and upper
95% HPDs
Mean
Lower and upper
95% HPDs
Mean
Lower and upper
95% HPDs
Lognormal minima only,
s=0.5, m=1.5
Lognormal minima only,
s=0.5, m=2
Lognormal minima only,
s=0.5, m=2.5
Uniform
minima & maxima
631
375
625
615
564
504
473
530
326
261
495
460
399
346
632
409
628
619
582
529
499
553
383
314
523
490
435
382
633
445
629
621
597
553
522
574
442
373
549
521
472
422
575
345
527
519
390
325
289
358
182
135
325
292
263
242
620
264
610
592
532
450
405
492
248
187
456
416
350
293
636
480
636
633
596
561
541
565
411
349
538
504
448
394
Cauchy minima only,
p=0.1, c=0.5
640
473
601
582
486
442
415
437
210
164
397
362
305
262
Mean
606
354
572
550
465
413
380
420
195
146
381
347
290
250
556
245
521
499
414
349
311
373
152
105
336
307
261
239
624
293
617
600
555
472
429
519
287
220
483
446
380
323
636
523
636
635
608
580
565
587
468
405
563
537
490
444
Cauchy minima only,
p=0.1, c=1
642
467
621
598
518
473
449
469
237
191
426
388
322
271
613
360
583
560
482
431
398
435
207
157
395
358
297
253
565
250
532
504
429
368
330
384
154
110
347
315
265
239
627
325
621
604
575
502
454
545
350
265
512
477
417
361
636
571
636
635
618
598
585
602
543
481
584
563
524
486
Cauchy minima only,
p=0.1, c=2
643
467
632
609
536
492
466
486
257
206
444
404
333
279
616
366
588
565
490
441
408
443
215
165
402
364
301
255
572
260
539
507
436
379
338
392
158
114
353
319
266
239
528
211
515
501
366
287
258
332
152
93
307
286
254
239
584
372
530
514
398
338
295
361
189
145
326
292
264
243
533
242
516
499
372
300
264
336
152
105
307
282
250
239
Lower and upper
95% HPDs
Lognormal
minima & maxima
634
485
541
537
414
364
307
385
223
176
345
295
273
247
Uniform
minima & maxima
645
471
635
614
545
505
476
497
272
218
454
412
340
283
Mean
565
312
522
512
384
319
284
355
172
127
329
305
269
245
519
188
516
502
354
289
222
331
155
103
312
286
256
240
620
439
530
522
417
354
339
382
195
152
349
325
282
252
Skew-t
minima & maxima
637
501
543
531
418
377
316
387
229
191
345
300
277
250
567
323
521
507
384
323
287
349
169
126
322
296
262
242
518
190
515
499
350
284
230
323
152
95
307
275
248
238
624
457
531
517
420
364
346
376
194
154
342
317
278
248
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