1
Supplementary materials and methods
2
Character and taxon sampling
3
Initial taxon sampling aimed to maximize representation of orbicularian families at the generic
4
level. Outgroups were added trying to maximise representation of families of non orbicularian
5
entelegyne lineages, particularly the RTA clade and Eresoidea. Sequences downloaded from
6
GenBank were assembled in matrices together with newly generated data with the help of BioEdit
7
v 7.0.5.3 and Mesquite v 2.74 [1] programs. Taxa that were represented in GenBank only with
8
sequences from fast evolving genes (16S rRNA, cytochrome c oxidase subunit I) or just a single
9
gene overlapping with our gene sample were not considered. Information about taxa included in
10
the analysis and GenBank accession numbers is given in Table S1. Several additional sequences
11
became available after our analyses were at an advanced stage [e.g., 2] and these data were
12
therefore not included.
13
All sequences were submitted to BLAST (http://blast.ncbi.nlm.nih.gov/) against the GenBank nr
14
database and examined for potential problems such as contamination. Several problems were
15
encountered and the corresponding sequences were excluded from further analysis. Sequences of
16
the 28S rRNA of Nephila clavipes B (FJ525379), Pimoa sp. (FJ607545) and SYMP_03_MAD
17
(GU456867) resulted in BLAST hits that were inconsistent with respect to other spiders’ 28S rRNA
18
sequences. These three sequences were also extremely difficult to align and when submitted to
19
direct optimization analysis most of their length was not recognised as homologous to the
20
sequences of the other taxa in our matrix. We could not re-sample these specimens to sort out the
21
problem and their 28S rRNA data were not included in any of the analyses. The 18S rRNA
22
sequence of the linyphiid Pityohyphantes costatus (AY078675) was found to be a contamination
23
from a theridiid and was also excluded from the analysis. Holarchaeidae and Pararchaeidae
24
sequences [3] were included only in preliminary rounds of ML analyses to corroborate their
25
placement within araneoids. In addition, protein-coding sequences were translated to amino acids
26
and examined for unexpected stop codons.
27
Data matrices
28
All data were combined in a single data matrix that included a total of 291 taxa (‘Full_data_pre’).
29
This matrix was first analysed under ML criterion in order to test the araneoid placement of the
30
families Holarchaeidae and Pararchaeidae [3; 4]. These two families were then excluded from
31
subsequent analyses because they were represented by just a single species each and had a very
32
small data overlap with most of the taxa in the dataset. The resulting matrix (‘Full_data’) was used
33
as a reference for any further data manipulation: calculation of missing data, fragment overlap,
34
and leaf stability indices. The ‘Full_data’ matrix was evaluated under two different criteria and as a
35
result two sets of matrices were produced (Table S2). One was aimed to optimize fragment
36
overlap and minimize missing data, and the other was based on the leaf stability index. Data
37
fragments were defined for each gene based on the amplicons used to obtain its sequence. In the
38
case of wingless and histone 3 there is only one amplicon. When in all taxa several contiguous
39
amplicons were consistently present these ware treated as a single fragment. A graphical
40
representation of the genes and the corresponding fragments is given in Figure S1. Amplicon
41
fragments were used to access data overlap and completeness and do not necessarily coincide
42
with the partitioning of the data for the maximum likelihood analyses. Data partition schemes
43
used in the maximum likelihood analyses are defined in the corresponding sections below.
44
When using the two different criteria for matrix optimization described here, different taxa were
45
selected for exclusion (see Table S1). As a consequence, resulting matrices did not have the same
46
number of terminals and taxa composition. Direct comparison among trees resulting from these
47
matrices using topological indices is problematic. To compare results and quantify changes in
48
resolution we have used the ability of each data matrix to recover major orbicularian lineages and
49
the support values associated to them (Table S4).
50
51
Alignments
52
Multiple sequence alignments were carried out using the online implementation of MAFFT v. 6 [5]
53
available at http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ (note that at the time of writing
54
the present manuscript the MAFFT server has moved to a new address
55
(http://mafft.cbrc.jp/alignment/server/). Both L-INS-i and E-INS-i strategies were used. E-INS-i
56
option was used for ribosomal genes where several conservative regions (stems) spaced by
57
variable regions (loops) are expected to occur. Fewer amplicons in some of the 28S rRNA
58
sequences resulted in alignment artefacts due to the very high variability in some regions of this
59
gene. To overcome this problem, 28S rRNA sequences were split into two separate matrices in
60
accordance to the primers used to generate them. Each matrix was independently submitted to
61
MAFFT. In addition, because the two 28S rRNA fragments showed distinct variability they were
62
kept as separate partitions. After alignment, protein-coding genes were translated to amino acids
63
and checked for unexpected stop codons.
64
Maximum Likelihood analyses
65
Maximum likelihood analyses were carried out in RaxML-HPC v 7.2.7 [6] at the CIPRES portal
66
(http://www.phylo.org/sub_sections/portal/) [7]. Data were partitioned by gene with two
67
partitions for the 28S rRNA. In addition, protein-coding genes were partitioned by codon position
68
with the first two positions into the same partition. To optimize computational efficiency we have
69
used GTRCAT for the bootstrapping phase and GTRGAMMA for the final evaluation of the
70
likelihood. Model parameters were optimised independently for each partition. To estimate group
71
support 1000 bootstrap replicates were evaluated.
72
Parsimony analysis of the statically aligned data
73
TNT analyses were carried out in the computer program TNT v 1.1 [8]. A driven search combining
74
new technology algorithms using equal weights (i.e., tree drifting, mixed sectorial searches, and
75
tree fusing) was performed (50 initial addition sequences, initial level: 10, cycles of drifting: 10),
76
and stabilizing strict consensus five times (with default factor of 75). This is one of the most
77
efficient search strategies when dealing with large and more difficult datasets [9]. Most other
78
search settings were left as default values. Commands used were included in, and run from, a
79
script file, which was generated by modifying an automatically generated TNT batch file. The script
80
file contained the following commands (a basic explanation of sets of commands are provided, for
81
a detailed explanation of each setting, please refer to the program’s help):
82
Basic commands:
83
hold 80000; piwe-; const-; rseed1;
84
Search commands (ratchet not active, default commands are automatically created by default in
85
the TNT batch file, and were left here for the sake of reproducibility):
86
xm: noverb nokeep; rat : it 0 up 4 down 4 au 0 num 36 give 99 equa ;
87
88
89
90
Tree drifting settings:
dri: it 10 fit 1.00 rfi 0.20 aut 0 num 36 give 99 xfa 3.00 equa;
Mixed sectorial search settings:
sec: mins 45 maxs 45 self 43 incr 75 minf 10 god 75 drift 6 glob 5 dglob 10 rou 3 xss 10-
91
14+2 noxev noeq;
92
Tree fusing settings:
93
94
95
96
97
tf: rou 5 minf 3 best ke nochoo swap;
General search settings:
xm : level 10 nochk rep 50 fuse 3 dri 10 rss css noxss mult nodump conse 5 conf 75 nogive
notarg upda autoc 3 xmix; xm ;
xmult:;
98
Jackknife frequencies were calculated in TNT under equal weights by computing 4000
99
pseudoreplicates performing heuristic searches consisting of 10 random addition sequences,
100
followed by 10 iterations of TBR (tree bisection and reconnection), holding one tree (commands:
101
hold 80000; piwe-; const-; rseed1; mult: noratchet repl 10 tbr hold 1 ; resample jak repl 4000 freq
102
from 0 [mult];). Due to the large size of the data matrix and in order to speed up the analysis of the
103
jackknife calculations, we used a traditional search strategy in the re-sampling. Gaps were treated
104
conservatively as missing data.
105
Direct optimization
106
Dynamic optimization analyses were carried out in POY v 4.1.2.1 [10] on the computer clusters at
107
the University of Copenhagen and the PYRAMID cluster at The George Washington University’s
108
High Performance Computing Laboratory. All protein-coding genes were treated as prealigned and
109
alignments from MAFFT were used. We have used the combination of the following commands to
110
perform the tree searches:
111
set(exhaustive_do)
112
report (data, cross_references)
113
transform(tcm:(1, 1))
114
build(250)
115
swap(threshold:5.0)
116
select()
117
perturb(transform(static_approx),iterations:15,ratchet:(0.2,3))
118
select()
119
fuse(iterations:200,swap())
120
121
Use of other than equal costs for gaps (gap opening and gap extension) and substitutions resulted
122
in memory errors in both clusters to which we had access. Only when equal costs were used the
123
analysis did finish successfully. Both computing infrastructures differ significantly in hardware and
124
software setups, therefore the only possible reason for these receptive failures may be related to
125
the program (POY) and/or to the size of the dataset being analysed.
126
To estimate Jackknife supports under direct optimization we read the data files and the
127
corresponding most parsimonious trees in POY. Supports were calculated using the following
128
commands:
129
transform(static_approx)
130
calculate_support (jackknife:(remove:50, resample:1000))
131
report (supports:jackknife)
132
133
Molecular dating
134
The hypothesis of homogeneous rates of evolution among lineages was rejected by the likelihood-
135
ratio test [11]. Therefore for this dataset the use of a strict molecular clock is not appropriate and
136
we have used instead a relaxed uncorrelated lognormal clock model as implemented in the
137
program BEAST [12]. We used fossil species to calibrate the relaxed clock and to estimate
138
divergence times. All fossils used as constraints were selected in such a manner that they are well
139
spread throughout the phylogeny. Only the oldest fossils that can be assigned to monophyletic
140
groups with high support in our results were used. As a result some known fossils that belong to
141
lineages represented by a single taxon or fall within unstable clades with low support were not
142
included. We have chosen this very conservative approach to avoid introducing potential
143
additional errors in our analysis. Certain fossils that met most of the former requirements were
144
intentionally not used as calibration points but as an independent test of the dating results. These
145
were Oecobius (described from New Jersey amber [13]), Agelenidae (described form Baltic amber
146
[e.g., 14; 15]) and Hersiliidae (described from Myanmar amber [16]). The following fossils were
147
used to calibrate the clock: Oecobiidae (min age 135 Ma) based on the Lower Cretaceous spider
148
Lebanoecobius schleei [17]; Araneidae (min age 115-121 Ma) based on the species Mesozygiella
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dunlopi described from Lover Cretaceous amber from Spain [18]; Tetragnathidae (min age 125-135
150
Ma) based on the fossils Macryphantes cowdeni [19] and Huegina diazromerali [20] both from the
151
Lower Cretaceous deposits in Spain; Linyphiidae not including Stemonyphantes (min age 125-135
152
Ma) based on a linyphiine species described form Lebanese amber [21]; Pimoa (min age 35-40 Ma)
153
based on several fossil species described from Baltic amber [17; 22]; Nephila (min age 165 Ma)
154
based on the recently described Nephila jurassica [23]. Macryphantes cowdeni is described from
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somewhat older deposits than H. diazromerali and the assignment of both species to
156
Tetragnathidae remains problematic. The preservation of both specimens is poor and there are
157
just a few characters that have been used to argue for a tetragnathid placement. In that case we
158
have used the interval between the youngest possible ages of these taxa to define a more
159
conservative minimum age constraint. The oldest linyphiid fossil shares some synapomorphies
160
with the linyphiine species but not with Stemonyphantes; the latter has been hypothesized as the
161
sister lineage of the remaining taxa in the family Linyphiidae (note that in our results we failed to
162
recover this relationship; see also discussion below). Therefore we have used the age of this
163
linyphiid fossil as a minimum age constraint for the well-supported clade containing all linyphiids
164
except Stemonyphantes. In the case of Oecobiidae we used the upper bound of the fossil dating as
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a minimum age constraint instead of the lower bound because this resulted in a more congruent
166
estimate for the minimum age of the crown Oecobius species, as suggested by the fossil record.
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None of the constraints has been implemented as a point calibration and possible errors were
168
accounted for in all cases, hence fossil cross-validation is not strictly necessary. Nonetheless, we
169
run two additional analyses removing one calibration point at a time. We run analyses without
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Nephila and without the Tetragnathidae species constraints, respectively. Estimated divergence
171
times of these lineages were then checked for congruence with their fossil record.
172
All fossils were treated as stem lineages with respect to the crown groups with which they share
173
putative synapomorphies. The fossil age was then used to set a minimum age constraint for the
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split between the fossil and the rest of the taxa in the crown group [24; 25]. Since the exact
175
placement of the fossil over the stem is uncertain, hence the exact age of divergence with the
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crown group, we have used probability distribution functions (either exponential or logarithmic)
177
that allow older divergence ages in order to account for that uncertainty. This approach also takes
178
into account the possibility that the oldest known fossil is most likely not the mrca of its lineage.
179
For the BEAST analysis, the best ML tree from the RaxML analysis of the ‘datasetv1_1’ dataset (see
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Table S2) was used as a starting tree. The dataset was partitioned by genes reflecting the partition
181
scheme used in the ML analysis and a GTR + G model (the same as in the ML analyses) was used
182
for each partition. A birth-death speciation model was assumed for the tree prior. Two analyses of
183
BEAST were run, one with exponential distribution for the probability density of the tmrca prior
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and one using a lognormal distribution with the calibration points as given in Table S3. Parameters
185
were chosen in such a way that 95% of the prior distribution lies between the minimum (the offset)
186
and the maximum values of the corresponding fossil dating.
187
Web characters and character optimization
188
Web architecture was scored following the coding of BEA. The only difference is the replacement
189
of the state ‘webless’ with the state ‘no foraging web.’ This state refers to the cases where webs
190
are absent or they are not used for prey capture but serve other functions (e.g., the nursery webs
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of some pisaurids). It is important to stress that neither the ‘webless’ nor the ‘no foraging web’
192
states represent necessarily homologous conditions in all species to which this scoring is applied,
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as absence of a feature does not necessarily imply homology. In fact, the same state (absence of a
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web for prey capture) may be the result of very different and independent processes and may
195
therefore violate the homology requisites. On the other hand, it is also clear that such an absence
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could be potentially synapomorphic. For example, it seems logical to hypothesize that the absence
197
of webs in pirate spiders (Mimetidae) is a putative synapomorphy of this family (or synapomorphic
198
for Mimetidae plus Malkaridae). Our goal is to map variation in web architecture on the optimal
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phylogenetic trees to gain insights on the evolution of these traits.
200
201
Supplementary results and discussion
202
All best trees from all analyses are available in the Best_trees.nex file in Mesquite format. This file
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also contains the web character dataset used in our analyses. In addition, majority rule trees from
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bootstrap and jackknife calculations under the different analytical criteria are also available as a
205
pdf file Supports.pdf.
206
207
Discussion
208
Divergence time estimates
209
Analyses in BEAST under both exponential and lognormal error distribution for the tmrca prior
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gave very similar results with overlapping confidence intervals. We have used the results from the
211
analyses with exponential priors (Fig. 2) to guide the discussion. The estimated divergence times of
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the three lineages available as independent contrast of the results (Oecobius, Agelenidae and
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Hersiliidae) were highly congruent with their ages suggested by the fossil record. Furthermore, the
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two cross-calibration runs resulted in overlapping age estimates for the nodes involved. There is
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only one case of major discordance between the fossil record and our dating results - the araneoid
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family Theridiidae. Although no theridiid fossils are known from the Mesozoic, our results suggest
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a Jurassic origin for this lineage. There are numerous theridiid fossils described from Baltic and
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Dominican ambers where they are one of the dominating spider groups, but no theridiids have
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ever been found as Cretaceous amber inclusions. Because there is a high diversity of theridiid
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genera in Baltic amber and because the family also occurs in the slightly older Lowermost Eocene
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amber from Paris (specimens not described, see [26]), it seems logical to infer that the family first
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appeared before this time, despite their intriguing absence from Cretaceous ambers. The spider
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fossil record is rather fragmentary, particularly for non-amber deposits. Small-sized species, like
224
many theridiids, preserved in sedimentary deposits with the level of morphological detail needed
225
for identification are uncommon. Furthermore, most amber deposits are found in the northern
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hemisphere, and Cretaceous amber deposits had been found primarily in Eurasia and North
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America (more recently 93 to 95 million-year-old amber deposits have been discovered in Ethiopia,
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the first major discovery of its kind from the African continent; [27]). The paucity of Cretaceous
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amber deposits from areas that formed part of Gondwana may help explain the perplexing
230
absence of Mesozoic theridiid fossils and the discrepancy between our dating results and the
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known fossil record.
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233
Taxonomic Discussion
234
In this section we expand the discussion of the taxonomic and systematic implications for
235
Orbiculariae resulting from the phylogenetic analyses presented in the main body of the
236
manuscript. Unless otherwise stated, membership and composition of higher level groups are
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discussed for extant taxa only [see 28for reviews of fossil spiders; 29]. We have chosen the results
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of the ML analyses of an almost complete data matrix (dataset1_v1 with 272 taxa) to guide this
239
discussion (Fig. 1).
240
Family composition of Orbiculariae
241
Orbicularians are composed by the superfamilies Deinopoidea (Deinopidae and Uloboridae) and
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Araneoidea (19 families) and the family Nicodamidae. Araneoidea includes the following families:
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Anapidae, Araneidae, Cyatholipidae, Holarchaeidae, Linyphiidae, Malkaridae, Mimetidae,
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Mysmenidae, Nephilidae, Nesticidae, Nicodamidae, Pararchaeidae, Pimoidae, Symphytognathidae,
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Synaphridae, Synotaxidae, Tetragnathidae, Theridiidae, and Theridiosomatidae.
246
Orbicularian monophyly and composition has been debated extensively in recent years [e.g., 3; 30;
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31-33]. Rix et al. [3] found in their sequence data strong support for the monophyly of Araneoidea
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(including representatives of Malkaridae, Mimetidae, Holarchaeidae and Pararchaeidae) but the
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interrelationships of the araneoid families were largely unresolved in his analyses. They sequenced
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fragments of the 18S and 28S ribosomal RNA genes for 48 species in 14 spider families (including
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representatives of 10 araneoid families), but the main goal of their study was to infer the limits
252
and phylogeny of the anapid subfamily Micropholcommatinae (and consequently about half of
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their species were anapids). Our analyses include representative species of 21 orbicularian families
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and of 49 araneomorph families. Our data provide the first empirical support for the monophyly of
255
Orbiculariae based exclusively on nucleotide sequence data for a broad higher-level taxon sample.
256
The results of our analyses refute the placement of the RTA clade within orbicularians, as
257
proposed by the recent molecular analysis of BEA.
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Deinopoidea
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The representatives of both Uloboridae and Deinopidae each form a monophyletic group.
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Although Deinopoidea is monophyletic in the full dataset the support is low. Variations of the full
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dataset do not recover the monophyly of Deinopoidea: in the preferred topology (Fig. 1)
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Uloboridae is sister to Araneoidea plus Nicodamidae, rendering Deinopoidea paraphyletic.
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Nicodamidae
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The family Nicodamidae is peculiar in that it contains both cribellate and ecribellate species [34].
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Although nicodamid monophyly has never been robustly established with morphological data,
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their phylogenetic placement has been considered critical to understand the evolution of orb
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weavers [30; 31]. BEA total evidence dataset suggested that nicodamids are monophyletic and
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sister to Araneoidea, although their molecular partition alone did not support the monophyly of
269
nicodamids because their cribellate representative (Megadictyna) was placed as sister to
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Theridiidae. Ecribellate and cribellate nicodamids form a clade in 13 of the 24 analytical variations
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that we explored. Our full dataset supports nicodamid monophyly under ML and parsimony except
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under DO. Under ML and DO analyses of dataset_v1 (see Table S4) nicodamids are monophyletic
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and the sister group of Araneoidea (trees included in the supplementary nexus file). In none of our
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analyses Megadictyna (or any other nicodamid) clusters with Theridiidae [33; 35]. Although the
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preponderance of molecular analyses support nicodamid monophyly and its placement as the
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sister lineage of Araneoidea this issue has not been robustly resolved yet.
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Araneoidea
278
The monophyly of araneoids is supported by all variations of the data matrix with support values
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ranging from moderate (69) to high (98). In addition to the traditional families [see 30],
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Araneoidea also includes the families Malkaridae, Mimetidae, Holarchaeidae and Pararchaeidae.
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While the monophyly of some of the araneoid families is supported by resampling techniques (see
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comments below), none of the deeper nodes within Araneoidea receive support, leaving most
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interfamilial relationships poorly resolved. Collapsing all interfamilial nodes within Araneoidea
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with values below the rather modest bootstrap of 75% would leave a completely unresolved
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hypothesis of interfamilial relationships (with the exception of the clade Mimetidae plus
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Tetragnathidae).
287
Araneidae and Nephilidae
288
Araneidae monophyly (including the oarcines and excluding Arkys) is very well supported by all
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analytical treatments. Araneids are sister to the lineage of Nephila and its relatives, as suggested
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by recent cladistic analyses [e.g., 36; 37]. Oarcines, traditionally considered members of
291
Mimetidae (e.g., Platnick & Shadab 1993), are monophyletic and are always placed within
292
Araneidae, never close to Mimetidae (Oarcinae, NEW FAMILY PLACEMENT). Oarcinae includes
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two genera from Chile and Argentina, both represented in our analyses, which “have long been
294
controversial and difficult to place” [38]. These results suggest that the distinctive leg spination
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pattern and cheliceral peg teeth of mimetids and oarcines has evolved independently. Arkys, our
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sole representative of a lineage of webless, sit and wait predators, the Arkyinae (currently placed
297
in Araneidae), is the sister group of Tetragnathidae (see comments under ‘Tetragnathidae’). None
298
of our analyses supports an araneid placement for Arkys. The placement of the clade composed by
299
Nephila and its close relatives (Nephilidae or Nephilinae) as tetragnathids [30; 39-41], a hypothesis
300
that had been proposed on the basis of morphological and behavioural data, is not supported by
301
our molecular analyses or by recent combined molecular and morphological analyses [e.g., 37].
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For most of the twentieth century “Nephilinae was considered a subfamily of Araneidae” [42].
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Recently, Nephilinae was raised to family rank (“Nephilidae”) by Kuntner [43]. This change in rank
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in the Linnaean hierarchy was justified on the finding that Nephilinae “does not group with
305
Tetragnathidae and thus cannot continue to be catalogued there” [43: 24]. Recent analyses [33; 36;
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37; 44] suggest that nephilines are closely related to araneids (regardless of what Linnaean rank
307
they are assigned). The inclusion of Nephilinae within Araneidae is by no means a new idea, as it
308
has been proposed on the basis of morphological features [e.g., 45; 46-48], behavioural data [e.g.,
309
49], nucleotide sequences [e.g., 50] and combined morphological and molecular analyses [e.g., 36;
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37]. The results of our analyses would support returning the nephilines to its original subfamily
311
rank within Araneidae to better represent its phylogenetic position. Under such a revised
312
circumscription, the family Araneidae (including Nephilinae) could be diagnosed by the following
313
combination of characters: PMS with an aciniform brush; female chelicerae with denticles; female
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chilum; hirsute female carapace; labium of pentagonal shape; sustentaculum; and vertical orb
315
webs. These characters and their taxonomic distribution, including exceptions and instances of
316
homoplasy, are described elsewhere [e.g., 30; 36; 37; 42; 51; 52]. Nomenclatural issues aside,
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revealing the sister group of Nephila is important for studies of comparative biology because of
318
the status of several species of this genus as model organisms in arachnology. Our results also
319
corroborate prior morphological [41] and combined morphological and molecular data analyses
320
[36; 41; 53] in suggesting that the clade composed by Herennia plus Nephilengys is the sister group
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of Nephila, and not Nephilengys [e.g., 54].
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Malkaridae
323
Malkarids are very poorly known and include eleven described species distributed in Chile and
324
Australia [55] and New Zealand, although the bulk of the diversity of the family remains
325
undescribed. Malkaridae has been suggested as the sister group of Mimetidae [47] based on the
326
leg spination pattern and on the absence of web-building. However, as Platnick and Forster [56]
327
have stated, “much descriptive and revisionary work on both groups is needed before the
328
monophyly of the Mimetidae can be regarded as clearly established; the possibility remains that
329
the Malkaridae may represent only a highly autapomorphic subgroup of mimetids.” Several
330
morphological synapomorphies support the monophyly of Malkaridae, including a conductor
331
flange in the male palp, deep alveolations on the carapace and the presence of a small
332
unsclerotised area behind the epigastric furrow [56; 57]. Our analyses recover a Perissopmeros
333
plus Carathea malkarid clade [as in 3] with high support, but this lineage is never sister to Malkara.
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None of our analyses support a sister group relationship between malkarids and mimetids.
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Mimetidae
336
Our analyses included seven mimetid species. As discussed above, the four oarcine
337
representatives form a clade nested within Araneidae and thus are not closely related to the other
338
two mimetids in our sample. The “true” mimetids (two species) form a clade sister to
339
Tetragnathidae plus Arkys (as in BEA’s analysis). The results also suggest that mimetids and
340
malkarids have abandoned web-based foraging strategies independently.
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Tetragnathidae
342
Tetragnathid monophyly is robustly supported and the internal relationships are congruent with
343
those proposed by recent analyses of combined morphological and molecular data [36; 37]. The
344
sister group of Tetragnathidae is Arkys (currently in Araneidae), a hypothesis also suggested by the
345
analysis of BEA. The composition and systematic placement of Arkynae has a long a controversial
346
history [reviewed in 51; 58]. For example Arkys has been placed in Thomisidae [59], Araneidae [60;
347
61], Mimetidae [62] and Tetragnathidae [45], having undergone many familial transfers numerous
348
times. The cladistic analyses of Scharff and Coddington [51] and Framenau et al. [58](the latter
349
being a revised version of the former) place the Arkynae within Araneidae. The morphological data
350
of BEA also placed Arkys as araneid but given the high degree of incompleteness of that matrix
351
(54% of all the cells and 84% of the cells of Arkys are ‘missing entries’) such hypothesis is very
352
poorly supported. The morphological, molecular and combined analyses of Dimitrov and Hormiga
353
[37] also refuted an araneid placement for Arkys, which their data placed as either sister to
354
Tetragnathidae or to Mimetidae.
355
356
Symphytognathoids
357
The informal label ‘symphytognathoids’ was proposed by Griswold et al. [30] for a clade that
358
included the families Theridiosomatidae, Mysmenidae, Anapidae and Symphytognathidae. The
359
monophyly of symphytognathoids (represented by a total of 37 species in four families) is never
360
recovered in our analyses. Lopardo et al.’s [63] analysis, with a much denser symphytognathoid
361
taxon sampling, also failed to recover this clade when only DNA characters were analysed.
362
Although they found symphytognathoids monophyletic under four parameter sets (and to include
363
the family Synaphridae as well), its monophyly was not obtained in any molecular partition
364
analysed as non-symphytognathoid species were consistently placed within this group in no
365
consistent pattern and with variable support values. Our analyses, using a much denser outgroup
366
sampling, suggest that Lopardo et al.’s [63] results might not be an artefact of their outgroup
367
sampling. The puzzling placement of Gertschanapis within the Araneidae clade in BEA’s analysis,
368
their only symphytognathoid representative, is not supported by our data (or any other analyses)
369
and it seems that this grouping may be a taxon-sampling artefact.
370
Symphytognathidae, represented by four species, is monophyletic in our analyses, but none of the
371
other symphytognathoid families are recovered as clades. Although Mysmenidae, represented by
372
15 species, is not monophyletic, this is due to a single species (Trogloneta sp.) jumping out of an
373
otherwise relatively well supported lineage with all other mysmenids. Theridiosomatidae and
374
Anapidae are polyphyletic, although the support values of most of the nodes involved in their
375
polyphyly are very low.
376
Holarchaeidae and Pararchaeidae
377
Holarchaeidae and Pararchaeidae had been placed in Forster and Platnick’s [64] Palpimanoidea.
378
Our results corroborate the araneoid placement of Holarchaeidae and Pararchaeidae [3; 4]. None
379
of the analytical treatments that we explored found a close relationship between these two
380
families suggesting that its members may have abandoned web-based foraging strategies
381
independently. In our analysis Holarchaea is sister to a clade composed by two Australian anapids,
382
and this lineage receives high bootstrap support (90). This analysis was not designed to thoroughly
383
test the composition of Palpimanoidea sensu Forster and Platnick [64]. We included only one
384
Palpimanidae representative (Ikuma sp.) and no arachaeids, mecysmaucheniids, stenochilids or
385
huttoniids, but this question stands inextricably linked to the limits of Araneoidea. Despite these
386
limitations, the molecular data provide evidence that Pararchaeidae (represented by
387
Westrarchaea spinosa) and Holarchaeidae (represented by Holarchaea sp.) are nested within
388
Araneoidea although does not resolve their exact placement within the superfamily. Rix and
389
Harvey [65] pointed out that if pararchaeids were araneoids, they would be the only known
390
lineage that possessed two ALS major ampullate silk gland spigots (either by plesiomorphic
391
retention or by secondary reversal). They also point out that the absence of a deep furrow on the
392
ALS of pararchaeids, between the ampullate and piriform spinning fields is “extremely unusual for
393
the Araneoidea, although Lopardo et al. (2007) noted a similar morphology in Synaphridae.”
394
Unfortunately no sequences of synaphrids exist to test the propinquity of this family to
395
pararchaeids. We fully agree with Rix and Harvey’s [65] conclusion that additional research is
396
needed to satisfactorily explain character conflict and the cladistic position of these two unusual
397
and enigmatic families.
398
399
Nesticidae
400
Nesticid monophyly is very well supported, with a high bootstrap value (100). In our analyses the
401
family was represented by Nesticus cellulanus and two Eidmannella species. The specimen labelled
402
‘Nesticus sp.’ is clearly not a nesticid, but has been included in the analyses because its sequence
403
data have been used in other published analyses. Although the sister group relationship between
404
Nesticidae and Theridiidae is well supported on morphological and behavioural grounds [e.g., 30;
405
35; 66; 67] such clade in not recovered by any of our analyses. BEA did not include any nesticid
406
representatives in their analyses.
407
408
Theridiidae
409
The results of our analysis largely mirror those of Arnedo et al. [68]. Much of the theridiid
410
sequence data that we analysed have been taken from their work. The monophyly of Theridiidae
411
receives a modest resampling support value (71) but many of the internal nodes are weakly
412
supported. Latrodectines are monophyletic and sister to a clade with all the remaining theridiid
413
representatives. The Lost Colular Setae clade is sister to an Anelosimus clade. Hadrotarsines are
414
monophyletic, nested deep inside Theridiidae, and sister to the Spintharinae clade. The four
415
Argyrodinae representatives are also monophyletic but the sistergroup relationship of this
416
subfamily to Phoroncidia is only weakly supported and unstable. Phoroncidia has a fairly long
417
branch, both for the nucleotide data analysed here and for morphological characters [35]. The
418
monophyly of Pholcommatinae sensu Agnarsson [35] (represented here by five species plus
419
Styposis) is not supported by our analyses [or those of 68] but this is not surprising as this was the
420
clade in Agnarsson’s analyses that was most sensitive to data perturbations.
421
422
Synotaxidae
423
Our analyses only included sequences of a single synotaxid representative (Synotaxus waiwai) and
424
thus testing the monophyly of the family was not possible. The monophyly of this small araneoid
425
family [14 genera and 76 species described; 55] is supported by morphological features of the
426
male genitalia [30; 67; 69]. The exact placement of synotaxids among araneoids is far from clear,
427
as different analyses and datasets have provided different answers [e.g., 30; 35; 68-70]. Although
428
Synotaxus has been included in some molecular analyses [68; 70], no representatives of the other
429
two synotaxid subfamilies [namely, Physogleninae and Pahorinae; see 67] have ever been included
430
in a molecular study. The ML tree of the complete data placed Synotaxus in a clade that included
431
the nesticid lineage and two species of anapids, but with very low support values. In the results of
432
the analysis chosen to guide the systematics discussion (dataset1_v1) Synotaxus jumps to an
433
unsupported clade that includes micropholcommatines, malkarids and Epeirotypus. Testing the
434
morphological hypotheses proposed for both the monophyly and the placement of this family will
435
have to wait for a much more thorough taxon sampling as well as additional genetic data.
436
437
Cyatholipidae
438
Cyatholipidae are another enigmatic group whose monophyly is well corroborated on
439
morphological grounds [e.g., 71] but whose exact placement among araneoids remains a mystery.
440
As in the case of Synotaxidae, different analyses and datasets have provided different solutions to
441
this problem (see refs. for Synotaxidae). Our two cyatholipid representatives form a clade with
442
high support value nested within a large lineage that includes all the Linyphiidae and Pimoidae
443
species, with Cyatholipidae being the sister group of a clade with all linyphiids except
444
Stemonyphantes. All the basal internal nodes involved in this hypothesis have low support values.
445
Like linyphiids and pimoids (and some synotaxids), cyatholipids build foraging sheet webs.
446
447
Linyphiidae and Pimoidae
448
Our results are consistent with the recent work of Arnedo et al. [70], the source of most of the
449
data. As discussed in the previous section, the placement of Stemonyphantes and of the
450
Cyatholipidae clade are in conflict with hypotheses based on morphological data [reviewed in 70],
451
but none of the involved nodes have high support. The molecular data corroborate the placement
452
of the enigmatic North American species Nanoa enana as the sister group of the Holarctic genus
453
Pimoa, as proposed by Hormiga et al. [72] based on morphological evidence.
454
455
Supplementary Figures legends
456
Figure 1S. Graphical representation of gene fragments overlap. Green rectangle – sequence
457
available; Gray rectangle – no data.
458
Supplementary tables legends
459
All tables are included the file Tables_S1_S4.xlsx
460
Table S1. Species, family and GenBank accession numbers for the sequences used in the present
461
analyses. Accession numbers: NA = no sequence available (missing); * = new sequences from this
462
study. The last eight columns represent taxa that were excluded in each data perturbation. When
463
data overlap and completeness was used as a criterion an X denominates excluded taxa. When
464
leaf stability was used as criterion the leaf stability of the excluded taxa multiplied by 100 is given.
465
Table S2. Different matrices used in the analyses and criteria for taxa exclusion.
466
Table S3. Implementation of the fossil constrains for the molecular clock analyses.
467
Table S4. Support for the monophyly of the major clades in the different analytical treatments and
468
taxon sets. Orbiculariae includes Nicodamidae; Araneidae includes Oarcinae; Tetragnathidae
469
contains Arkys. * - some taxa were placed within the orb weavers. Numbers indicate bootstrap
470
support for the clades. For Orbiculariae bootstraps are shown even if they are less than 50.
471
Other supplementary files
472
Best_trees.nex – contains all optimal trees form all analytical variations. The file also includes the
473
web character scores used in ancestral state reconstructions.
474
Supports.pdf – Contains the following bookmarks: ML_bootsraps – includes the ML trees from
475
RaxML for all data matrices with all bootstrap > 50 shown; DO_jackknife – includes the MP
476
consensus trees from jackknife analyses under DO with all values > 0.50 (50) shown; MP_jackknife
477
– includes the results from the jackknife resampling in TNT under MP. Jackknife is calculated as
478
both proportions and groups frequencies.
479
480
Supplementary references
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