Blender as a tool for paleontologists with a case study on extinct arachnids

13 Pages·2014·1.18 MB·English

The walking dead: Blender as a tool for paleontologists with a case study on extinct
arachnids
Author(s): Russell Garwood and Jason Dunlop
Source: Journal of Paleontology, 88(4):735-746. 2014.
Published By: The Paleontological Society
DOI: http://dx.doi.org/10.1666/13-088
URL: http://www.bioone.org/doi/full/10.1666/13-088
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JournalofPaleontology,88(4),2014,p.735–746
Copyright(cid:2)2014,ThePaleontologicalSociety
0022-3360/14/0088-735$03.00
DOI:10.1666/13-088
THE WALKING DEAD: BLENDER AS A TOOL FOR PALEONTOLOGISTS
WITH A CASE STUDY ON EXTINCT ARACHNIDS
RUSSELL GARWOOD1 AND JASON DUNLOP2
1SchoolofEarth,AtmosphericandEnvironmentalSciencesandTheManchesterX-RayImagingFacility,SchoolofMaterials,Universityof
Manchester,Manchester,M139PL,UK,,[email protected].;and2Museumfu¨rNaturkunde,LeibnizInstituteforResearch
onEvolutionandBiodiversityattheHumboldtUniversityBerlin,D-10115Berlin,Germany,,[email protected].
ABSTRACT—This paper serves two roles. First, it acts as an introduction to Blender, an open-source computer graphics
program,whichcanbeofutilitytopaleontologists.Tolessenthesoftware’sotherwisesteeplearningcurve,astep-by-step
guide to create an idealized reconstruction of a fossil in the form of a three-dimensional model in Blender, or to use the
softwaretorenderresultsfrom‘virtualpaleontology’techniques,isprovidedasanonlinesupplementaldatafile.Second,
here we demonstrate the use of Blender with a case study on the extinct trigonotarbid arachnids. We report the limb
articulations of members of the Devonian genus Palaeocharinuson the basis of exceptionally preserved fossils from the
Rhynie Cherts of Scotland. We use these newly reported articulations to create a Blender model, and draw comparisons
withthegaitofextantarachnidstoproduceasaccuratearepresentationofthetrigonotarbidflexingitslimbsandwalking
as possible, presented in additional online supplemental data files. Knowledge of the limb articulations of trigonotarbid
arachnidsalsoallowsustodiscusstheirfunctionalmorphology:trigonotarbids’limbsandgaitwerelikelycomparableto
extant cursorial spiders, but lacked some innovations seen in more derived arachnids.
INTRODUCTION the Scottish Rhynie and Windyfield cherts that document their
BLENDER (BLENDER.ORG) is an open source, freely available, limbanatomy insome detail(e.g.,Dunlopet al., 2009;seealso
below). This facilitates an accurate and reliable reconstruction
and cross-platform 3-D computer graphics application
of the limb articulations, and through comparison with
maintained and developed by The Blender Foundation. It is
morphology (Shultz, 1989) and walking gaits in modern
versatile, allowing users to create, import, and modify 3-D
arachnids (Wilson, 1967; Ward and Humphreys, 1981; Shultz,
objects, then light, color and texture, and finally raytrace the
1987;Biancardietal.,2011;SpagnaandPeattie,2012)wehave
resulting models. It also provides the ability to animate 3-D
created an animated Blender model that we hope yields a
objects, and edit videos, in addition to many more complex
realistic impression of how these Paleozoic animals may have
options geared towards detailed, photo-realistic raytracing
walked in life.
which are beyond the scope of most paleontological applica-
tions. Blender was first released under a GNU license in 2002
BACKGROUND
andoverthelastdecadehasdevelopedtwoprimarycapacitiesin
Trigonotarbids.—Members of the extinct arachnid order
thepaleontological community.Anumberofauthorshaveused
Trigonotarbidasuperficiallyresemblespiders,butpossessednine
Blender to manually model meshes, creating raytraced, opisthosomal tergites divided into median and lateral plates, and
idealizedreconstructionsoffossilorganisms(Stein,2010;Haug lacked silk-producing spinnerets (Garwood et al., 2009; Posch-
et al., 2011, 2012; Stein and Selden, 2012; Haug and Haug, mann and Dunlop, 2011). Trigonotarbids are found among the
2012; see also Background discussion below). By contrast, earliest terrestrial animal communities, dating back to the late
others have used Blender as a means to produce high-quality Silurian(Prˇ´ıdol´ı;Dunlop,1996),andwerethusprobablyamongst
figures for publication of CT-scanned data, following process- thefirstpredatorsonland.NumerousDevonianfossilsalsoexist,
ingwithothersoftwaresuites(GarwoodandSutton,2010,2012; including three-dimensional specimens from the Rhynie and
Garwoodetal.,2011,2012;Spenceretal.,2012;Zamoraetal., WindyfieldChertsofScotland(seebelow),aswellasothermore
2012; Giles and Friedman, 2013). Despite increasing applica- conventional impression fossils from Alken an der Mosel in
tions within the paleontological community, and recognition of Germany (Poschmann and Dunlop, 2010), and some adjacent
the utility of 3-D reconstruction in all its forms (Sutton, 2008; localities, and Tredomen in Wales (Dunlop and Selden, 2004).
More than sixty trigonotarbid species are known though this is
Garwood et al., 2010), 3-D software—and arguably Blender in
likely to be an overestimate of their diversity. Authors such as
particular—has a very steep learning curve. No guides exist for
Fricˇ (1904) and Petrunkevitch (1949, 1953) erected genera and
the application of Blender in the scientific sphere.
species on the basis of superficial, often preservational,
Here we present a study completed with the assistance of
differences (Shear, 2000). Revisions have usually resulted in
Blender inwhichwedemonstrate the value and applicabilityof
the recognition of numerous synonyms (e.g., Garwood and
the software, coupled with an introductory tutorial (online
Dunlop, 2011). Nevertheless, the fossil record does suggests a
Supplemental Data file 1). This is intended to provide an
peak of diversity during the Upper Carboniferous (Dunlop and
accessible,step-by-stepguidetousingBlender,assumeslimited Ro¨ßler,2013,table1;Garwoodetal.,2009;Hyzˇny´ etal.,2013).
computational background knowledge, and is aimed at practic- During this period, numerous families developed heavy spines
ing paleontologists who are considering using Blender for their and dense dorsal tuberculation (Dunlop and Garwood, in press),
publications. We focus on an extinct group of arachnids called and increased the structural complexity of their carapace. Some
the trigonotarbids as our model organism, for which there are a may have practiced ambush predation (Garwood and Dunlop,
number of well-preserved and three-dimensional fossils from 2011).TheyoungesttrigonotarbidsdatefromtheLowerPermian
735
736 JOURNAL OF PALEONTOLOGY, V. 88, NO. 4, 2014
(Asselian and Sakmarian) and the cause of their eventual Blender uses a raytracing algorithm to render meshes, an
extinction remains unclear (reviewed by Dunlop and Ro¨ßler, approach which allows highly realistic shadow and lighting
2013). Factors may include climate change and loss of the coal effectstobecreated(Whitted,1980).Thisworksbymodelingthe
swamps, tetrapod predation, and competition from other arthro- path of light rays backwards from an imaginary camera or eye,
pods such as spiders. througheachpixelinavirtualscreen(Arvo,1986).Eachofthese
Trigonotarbidanatomy(bothexternalandinternal)isknownin raysisthentestedforintersectionwiththeobjectstoberendered
considerabledetail,thankslargelytotheexceptionallypreserved inascene.Thenearestobjectisidentified,andtheincominglight
chertspecimensnotedabove.Forfurtheraccountsofthesefossils at this point is combined with the material’s texture and
fromtheEarlyDevonianofScotlandseealsoHirst(1923),Hirst properties, after which the correct color for a given pixel can
and Maulik (1926), Shear et al. (1987), and Fayers et al. (2005). becalculated.Iftheobjectisreflectiveorrefractive,furtherrays
This remarkable material also yields internal details of both the arecastintothescene,andthepixelcolorcanbeupdated(Cook
foregut(Dunlop,1994a)andthelungs(ClaridgeandLyon1961; et al., 1984). This is repeated until a maximum number of
Kamenz et al., 2008). Of particular relevance to the present reflectionsormaximumdistancewithoutintersectionisachieved.
project is the preservation of external limb articulations, or
condyles,asdarkenedthickeningsofthecuticleonthepedipalps METHODS
and legs. In rare cases even sclerotized internal muscle tendons Fossils.—The Rhynie Chert fossils forming the basis of the
can be resolved—as figured for the pedipalp by Dunlop et al. present reconstruction can all be assigned to the genus Palae-
(2009, fig. 3d, 3f)—offering insights into the animal’s muscula- ocharinus Hirst, 1923 (Arachnida, Trigonotarbida, Palaeochar-
inidae) and are held in the Natural History Museum, London
ture.However,correspondingdetailsfromthewalkinglegswere
(NHM). The material iscurrently assignedto a range of species,
only previously figured in the unpublished thesis of Dunlop
most of which are probably synonyms (see comments in the
(1994b). We formally publish these observations here, and use a
unpublished thesis of Dunlop, 1994b). Pending formal revision,
RhynietrigonotarbidasamodelorganismforcreatingaBlender
we prefer to pool this anatomically homogenous material as
reconstruction with correct limb articulations. This enables an
Palaeocharinusspp.SpecimensIn24671,In24673,In27752,In
animation showing a pattern of anatomically accurate limb
27756–58 and In 27760 proved to be particularly useful in
flexion.
resolving the position of limb condyles (see also Fig. 1.1–1.16).
Meshes and raytracing.—A limited knowledge of the compu-
All fossils consist of slide-mounted chert fragments or thin
tational aspects of 3-D reconstruction will be beneficial to this
sections. The fragments were studied using a Leica MZ16A
introduction. As previously outlined, Blender has two primary
stereomicroscope with both incident and transmitted light. The
applications in paleontology: 1) mesh creation and 2) the high-
latter proved more suitable for understanding the three-dimen-
quality rendering of surfaces. The latter can be derived from
sionalanatomyofRhynieChertmaterialintranslucentfragments
tomography datasets through processing in a suitable software
such as the limbs presented herein. The software CombineZM
package (e.g., Avizo, VGStudio Max, Drishti or SPIERS) (for a
wasusedtocreate thepanels(Fig.1)bycombiningphotographs
full overview we direct the reader to Abel, 2012), or from
takenatmultiplefocaldepths(seeBercovicietal., 2009).Slide-
surfacescaptureddirectlyusing,forexample,photogrammetryor
mounted thinsections of chertwere examinedusing abiological
laser scanning. Whatever the source, Blender uses a raytracing
microscope. In a wider context, the Rhynie and adjacent
algorithmtorenderimagesfromsurfacegeometries.Thesethree-
Windyfield Chert is a world-famous fossil locality found in
dimensional polygon meshes allow the surface topology of an
Aberdeenshire, Scotland, U.K. These are a silicified sinter
objecttobemodeledthroughaseriesofinterconnectedtriangles,
deposits lain down in a hot springs environment, conventionally
each of which is defined by three points in space.
datedtotheLowerDevonian(Pragian)ofabout410Ma(Parryet
Ifcreatinganidealizedreconstructionofataxonfrommultiple al., 2011). For details of the geological setting and general biota
flattened fossils, or a variety of cross-sectional profiles through see Rice et al. (2002) and Fayers and Trewin (2004). These
samples, Blender allows the user to manually create and then localities represent one of the oldest terrestrial ecosystems, and
modify meshes, which can consequently be rendered from thus the fossil arachnids reconstructed here would have been
multiple angles or in animations for publications. This isusually among the oldest animals—and one of the first predators—to
achieved through the insertion of so-called ‘mesh primitives’ in walk on land.
the software (such as tubes and cubes) and the subsequent Blender.—Online Supplemental Data file 1 provides a general
modificationofthesethroughbothmanualeditingandtheuseof introduction to Blender. To accompany this, here we provide a
modifiers, i.e.,operations whichedit the mesh. Thisis knownas more detailed workflow, outlining the creation of the paleochar-
box-modeling (see online Supplemental Data file 1 for a more inid model presented herein. The only three-dimensionally
detailed outline). If, by contrast, data acquired through another preservedpaleocharinidtaxaarefromtheRhynieandWindyfield
technique needs to be rendered, the vast majority of methodol- Cherts, a deposit that is not conducive to analysis with CT.
Accordingly no meshes of paleocharinids exist, requiring one to
ogiesforthe3-Ddigitizationoffossilswillincludethecreationof
be created for the present study. When building reconstructions,
meshes prior to visualization (see further discussion in Sutton et
recycling is a valuable approach, and in the present study the
al., 2012). These can be exported from other software and
body of an anthracomartid trigonotarbid—a family which is
imported into Blender. Although some of these datasets will
probably closely related to palaeocharinids—was imported from
comprise multiple objects, and can have very high triangle
an existing STL file. Anthracomartids are similar in prosomal
counts—especially noisy CT data—Blender can successfully
morphology to paleocharinids. The model of the former could
importallbutthelargestmeshes,andawiderangeoffileformats.
thus be used as a basis for reconstructing the prosomal
For example, in tests for the current publication, a six-yr-old PC
morphology of the latter through manual editing of the mesh to
(12 GB RAM, NVIDIA GeForce GTX 280 graphics card) could approach the anatomy seen in the Rhynie and Windyfield Chert
load a mesh of 50 million triangles, and an ultrabook (4 GB fossils. In addition to saving time during modeling, this is
RAM, integrated Intel Graphics) could load 10 million. We note included here to demonstrate the utility of Blender’s import
hereasareminder,however,thatanotherpieceofsoftware(e.g., functions. We used the species Anthracomartus hindi Pocock,
Avizo, Amira, Mimics, SPIERS) is typically required to prepare 1911,herein.ThiswaspresentedinGarwoodandDunlop(2011),
data and convert to an appropriate mesh format. wherein a tomographic dataset was surfaced with SPIERS (see
GARWOOD AND DUNLOP—BLENDER, A UTILITY FOR PALEONTOLOGISTS 737
FIGURE1—LimbsofPalaeocharinusspp.fromtheEarlyDevonianRhynieChertofScotland.1,transversesectionofanopisthosomacontaininganarticulated
pedipalp,palaeocharinidNHMIn24685;2,achelicera,palpalandlegcoxaeinsection,showinggranulesonthepalpalcoxae,P.calmaniHirst,1923,holotype,
NHMIn24675;3,tibia,metatarsusandtarsus,showingmetarsus-tarsusarticulationasadarkspikeofcuticle,Palaeocharinussp.NHMIn27760;4,detailsof
thecheliceraeandpedipalp,includingthepatella-tibiaarticulationandmajorityofthepedpalppodomeres,P.rhyniensisHirst,1923NHMIn24673,holotype;5,
chelicerae,andproximalpedipalpandwalkinglegs,showingpalpalcoxalgranulationandsetae,Palaeocharinussp.NHMRC/080;6,trochanterandfemur
showingannulus,Palaeocharinussp.NHMIn24685;7,cross-sectionofalimb,P.scourfieldiHirst,1923,NHMIn27756;8,metatarsusandtarsusofawalking
limb,demonstratingthebaseoftheterminalclawsandaninternaltendonrunningupfromtheclawbase,Palaeocharinussp.NHMIn27758,9,tibiaandpatella
ofawalkinglimb,P.rhyniensisNHMIn24673;10,detailoftrochanterofwalkinglimb,P.rhyniensisNHMIn24673;11,almostcompletewalkinglimb,P.
rhyniensis NHM In 24673; 12, complete limb in section, Palaeocharinus sp.NHM RC/080; 13, large proportion of articulated limb above opisthosoma of
trigonotarbid,P.scourfieldiHirst,1923,NHMIn27756,14,detailoffemur-patellaarticulation,P.scourfieldi,NHMIn27756;15,coxaofwalkingleg2and3,
showingtrochanteralprojection,Palaeocharinussp.NHMRC/080;16,limbdetailshowingpatella-tibiaandtibia-metatarsusarticulation,P.scourfieldi.NHM
In 27756.Scale bars1–9, 0.25 mm;10, 0.1 mm;11–16,0.25 mm. Abbreviations: an¼annulus;c1¼coxawalking leg 1; c2¼coxa walkingleg 2; c-tr¼coxa-
trochanter articulation; ch¼chelicera; cl¼claw; en¼endite; fe¼femur; fe-pa¼femur-patella articulation; gr¼coxal granules; mt¼metatarsus; pa¼patella; pa-
ti¼patella-tibia articulation; pp¼pedipalp; pr¼trochanteral projection, op¼opisthosoma; st¼setae; ta¼tarsus; ti¼tibia; ti-mt¼tibia-metatarsus articulation;
tn¼tendon;tr¼trochanter;tr-fe¼trochanter-femurarticulation.
738 JOURNAL OF PALEONTOLOGY, V. 88, NO. 4, 2014
original publication for full methods). To modify the mesh, the results reported below, i.e., fixed coxae, coxa-trochanter largely
opisthosoma was selected: brushselect (shortcut C),was used to anterior-posterior and stiff, with trochanter-femur and femur-
highlight vertices at the posterior, ctrlþþenlarged the selection patella only allowing up and down movement, patella-tibia
until the majority of opisthosomal vertices were selected, and mobile with up and down movement and lateral rocking, tibia-
thenboxselect(B)wasusedtocreateasharpanteriormarginto metatarsus stiff with up down movement, metatarsus-tarsus
theselection.Delete(X)(cid:2)verticesremovedthese.Theremaining mobile withlimited up and downmovement andlateral rocking.
prosoma was then remeshed (Properties panel(cid:2)Object Modi- These were hard constraints in most cases, but on limbs with
fiers(cid:2)remesh, ocrtree depth 3, mode smooth, smooth shading).
limited movement in a given direction (in contrast to none), the
The reduced mesh was then modified manually to better match
stiffnesswasinsteadincreasedtoallowlimitedmovement(found
palaeocharinid morphology and create a more accurate recon-
in bone tab of the properties window). For each limb reverse
struction. The mesh was split along a sagittal plane, half was
kinematics was applied (shift þ I), with an empty (a Blender
deleted, the clypeus was extended by selecting median vertices
object whichdoesn’t render) as atarget allowingeasy animation
anddraggingwithhighproportionaleditingfalloff(PEF),andthe
of both the distal limbs (via the empty) and the proximal
lateral eye tubercle was moved posteriorly using a similar
podomeres (via the coxa) when walking. Limb is shown posed
approach.Coneswerecreatedandaddedasspinesontheclypeus
(Fig. 2.11). The limbs were then duplicated, resized as
(shift þ A(cid:2)mesh(cid:2)cone) then scaled/modified using methods
outlined in online Supplemental Data file 1. Median eyes were appropriate, and placed onto the model. Materials were applied
added (spheres, flattened) and positioned, as were lateral eye to create color, and the armatures were parented to a central
lenses. These were then united as a single mesh (ctrlþj), and a ‘bone’ to ease animation: this has the effect that the proximal
mirror modifier applied recreating the opposing half of the limbsfollowwhenthebodyadvances.Subsequently,toallowfor
carapace.Thetwohalveswerethenmanuallystitchedtoensurea the ‘alternating tetrapod’ gait typically used by living spiders
morphologically realistic join (by either merging vertices [altþ (e.g., Ward and Humphreys 1981; see discussion), the empties
m] or joining them with an edge then a face [f]). associated with the end of each of the limbs were parented to
The opisthosoma was created in its entirety, through steps anotherempty,allowingeachsetoffourlimbstobeanimatedin
illustrated in Figure 2.1–2.5. This was required because no unison for walking. Lights were added—four spots forming a
previouslyscannedtrigonotarbidspossessopisthosomalmorphol- square around the model with constant fall off and raytraced
ogysimilartothatobservedintheRhynieandWindyfield Chert shadow,andanteriorlyandposteriorlyfacinghemilamps.Afloor
paleocharinids. The opisthosoma was modeled on the basis of wasplacedinthescene(aplane)withatiledappearancethrough
various cross-sectional morphologies observed in slides of the a UV-mapped texture to show movement more clearly. A floor
chert taxa: a cube was added, scaled to the correct proportions, constraintwasaddedtothedistal-limbemptieswiththefloorasa
and then modified with numerous loop cuts (Fig. 2.1). The target, stopping the limbs from going through the plane. The
anterior-posterior dorsal sutures were created with three closely animations were then keyframed using the timeline—for the
spaced loop cuts, whereas each segment was created with two walking gait this employed the empties associated with each
loop cuts, one significantly smaller than the other (Fig. 2.2). quadruped.Thegrapheditorwasusedtoensure realisticratesof
Furtherloopcutswereusedtomoldtheventralopisthosoma,and movement between each keyframe. The forward movement for
ensure the correct cross section (Fig. 2.3, 2.4). A subdivision eachstepcyclewasequal,andthefloorwasanimatedmovingthe
surfacemodifierwasaddedtosmooththemorphologyandmake samedistanceintheopposingdirection.Thisallowedthewalking
itappearmorerealistic(Catmull-Clark,3subdivisions;Fig.2.5). animationtooccurinplaceandobviatetheneedtomovelighting.
Opisthosomaldetailssuchastheventralsacsandpygidiumwere Once a single step cycle was successfully animated, this was
created from modified spheres and joined. The opisthosoma was replicated using the DopeSheet Summary. The camera location
then manually stitched to the prosoma. The mesh was then androtationwasthenkeyframedtocreateavideowitharangeof
modifiedmanuallyoverseveraliterationstoensuregoodfitwith viewsofthetrigonotarbidwalking.Fortheflexingvideo,eachleg
the known morphology and published reconstructions of Palae- was manually keyframed in pose mode of blender, and then
ocharinus(e.g.,Fayersetal.,2005,fig.10).Opisthosomalmuscle renderedfromfourcamerasatdifferentangles.Fourfurtherspots
apodemes (dorsal depressions on each sternite) were created wereaddedforventralilluminationbyduplicatingthedorsalones
through the use of a boolean subtract modifier applied to the (shiftþD).
opisthosoma and a carefully positioned flattened sphere.
Limbs were created using similar methods to the opisthosoma RESULTS
Pedipalps.—Trigonotarbids possess pediform pedipalps, i.e.,
(Fig.2.6–2.11),basedonthemorphologyobservedinslides(Fig.
theyaresimilartothewalkinglegsandlackraptorialprojections
1),andthereconstructedarticulations(Figs.3,4).Cylinderswere
for prey capture as in whip spiders (Amblypygi) or whip
created, a number of loop cuts (Fig. 2.6) were added, and their
scorpions (Uropygi) or special organs for sperm transfer as in
position were then adjusted (Fig. 2.7). Individual vertices were
mature male spiders (Araneae). The trigonotarbid pedipalps are
edited with PEF enabled to create the dorso-ventrally asymmet-
smaller than the adjacent legs and comprise six elements: coxa,
ricalelements(Fig.2.8).Withtheadditionandeditingoffurther
trochanter, femur, patella, tibia and tarsus (Figs. 1.1, 1.4, 2;
loop cuts, and then application of a subdivision surface modifier
Dunlop, 1994b, pl. 8). The undivided tarsus bears a single claw
(Fig. 2.9), limbs matching the morphology shown in Figure 1
(or pretarsus), later shown to be the movable finger of a small
were created. An armature was then created. These are used in chelate structure in at least the Rhynie chert paleocharinids
Blender for rigging—they allow the user to create a control (Dunlop et al., 2009); similar to the condition in the pedipalp of
structure and then bind it to a mesh (skinning). When the the rare ricinuleids (Ricinulei). Articulations of the Palae-
armature, which consists of individual elements termed ‘bones’, ocharinus pedipalp (Fig. 3) based on Rhynie Chert material
is posed, it then deforms the mesh around it, allowing for more follow a format used by Shear et al. (1987) and Selden et al.
realisticandeasieranimation.Asingle‘bone’wasadded(shiftþ (1991).
A(cid:2) armature(cid:2)single bone), and then this was extruded (e) to ThepalpalcoxainPalaeocharinuspossessesfourorfivelarge,
createaseriesofsevenconnected‘bones’(sixforthepedipalps) heavily sclerotized granules on its ventro-mesal surface and a
corresponding to the appropriate limb podomeres (Fig. 2.10). setosemesalsurface(Fig.1.2,1.5).Itisunclearifthecoxaewere
Each element was given a realistic constraint on the basis of the fixed or free to move. The articulation of the palpal coxa-
GARWOOD AND DUNLOP—BLENDER, A UTILITY FOR PALEONTOLOGISTS 739
FIGURE2—BoxmodelingprocedurefortheopisthosomaandlimbsofthePalaeocharinusspp.modelpresentedinFigure6.Shownasbothwireframeand
solidmeshes.1–5,theconstructionoftheopisthosoma,modeledfromarectangle(1),throughtheadditionofloopcuts(2),mirroring(3)andmergingofthe
meshes(4),andthentheapplicationofasubsurfacemodifier(5);6–11,theconstructionandthenriggingofthelimbs;thesewereinitiallycylinders(6)towhich
loop cuts were added and resized (7); individual vertices were altered with PEF to create asymmetry (8), then a subsurface modifier was applied (9);
subsequentlyanarmaturewascreatedandapplied(10)allowingthelimbstobeposed(11).
740 JOURNAL OF PALEONTOLOGY, V. 88, NO. 4, 2014
FIGURE3—ArticulationsofthePalaeocharinuspedipalpbasedonRhynieChertmaterial,withsomedetailsfromShearetal.(1987)andDunlopetal.(2009).
SchematicformatfollowsthatusedbyShearetal.(1987)andSeldenetal.(1991).Abbreviations:co¼coxa;cl¼claw;fe¼femur;pa¼patella;ta¼tarsus;ti¼tibia;
tr¼trochanter.
trochanter joint is equivocal in the fossils: analogy with spiders (2009, fig. 3). A general reconstruction of the pedipalp in
suggestsmovementinboththeverticalandhorizontalplanewas Palaeocharinus is presented (Fig. 3).
possible. The trochanter-femur joint is an anterior-posterior, but Walking legs.—Trigonotarbids have pediform walking legs
composed of seven segments: coxa, trochanter, femur, patella,
obliquely angled articulation (NHM In 24671), and the femur is
tibia, metatarsus and tarsus (Fig. 1.12). The latter are sometimes
often the longest palpal podomere. The femur-patella joint is a
referredtoasthebasi-andtelotarsus(cf.Shultz,1989),giventhat
superior bicondylar hinge (NHM In 27752, Dunlop, 1994b, pl.
this is an adesmatic or ‘passive’ joint in which the articulation
44) and the patella is usually shorter than the femur. Its
between these elements lacks its own musculature, such that the
articulation with the tibia is a superior monocondylar hinge: metatarsus is thought to have simply divided off from the
NHMIn27752andIn24673suggestanarticulationpointslightly proximalendof thetarsus.GarwoodandDunlop(2011,text-fig.
off-center (Fig. 1.4). This could mean that the distal podomere 2) suggested that trigonotarbids probably adopted the usual
was orientated inwards in a slightly medial direction, but in terrestrial arthropod ‘hanging stance’; with an upward-pointing
general the pedipalp is not as well preserved as the legs in the femur, a principal bend at the femur-patella joint, and then
downward-pointing distal podomeres. Other fossils are often
Rhynie specimens and this interpretation should be treated with
preservedinthetypical arachnid‘deathposition’,withthelimbs
caution. The tibia-tarsus articulation of the palp is a superior
foldedtightlybeneaththebodyandthedistalpodomeresstraight.
monocondylar hinge (NHM In 27752, Dunlop, 1994b, pl. 44).
However, reconstructions of Carboniferous species such as
The rounded distal termination of the pedipalp tarsus, with its Eophrynus prestvicii (Buckland, 1837) (Dunlop and Garwood,
chelate pretarsal claw and associated (?depressor) tendon of the in press) inferred a more ‘plantigrade’ stance in life, i.e., the
movable claw finger was described in detail by Dunlop et al. tarsus is bent outwards and placed somewhat flatter on the
FIGURE4—ArticulationsofthePalaeocharinuswalkinglimbbasedonRhynieChertmaterial.SchematicformatfollowsthatusedbyShearetal.(1987)and
Seldenetal.(1991).Abbreviations:co¼coxa;cl¼claw;fe¼femur;mt¼metatarsus;pa¼patella;ss¼slitsensilla;ta¼tarsus;ti¼tibia;tr¼trochanter.
GARWOOD AND DUNLOP—BLENDER, A UTILITY FOR PALEONTOLOGISTS 741
FIGURE5—Thelyriformslitsensilla(ss)foundastwogroupsofsixventro-lateralslitsparalleltothelongaxisofdistalmetatarsus.1,NHMspecimennumber
In27756;2,NHMspecimennumberIn27760;3,NHMspecimennumberIn27757.Scalebar¼0.1mm.
ground.Thishypothesis issupported bycomparisons withliving al.,1991,text-fig.2).ThePalaeocharinuspatellaisusuallyshort
arachnids, whereby the metatarsus may have separated off from and varies little between legs. The patella-tibia joint has a
the rest of the tarsus to allow the distal tip of the limb to flex superior monocondylar hinge, clearly seen in NHM In 27756
outwards. Furthermore, the tarsal claws in the Rhynie Chert (Fig.1.13, 1.16) and In 24673(Fig. 1.9,1.11). Note that thereis
material (Fig. 1.8, 1.11) would be strongly displaced and risk nocorrespondingventralarticulationpointinPalaeocharinus,as
breaking if a purely digitigrade stance was used. In general, the is present in spiders (e.g., Clarke, 1986). In most trigonotarbid
legsoftrigonotarbidstendtobequitehomogeneousandsimilarin groups,thetibiaisthesecondlongestpodomereand,incommon
robustness and length, although the fourth legs were usually withthefemur,itislongerinlegs1and4.Towardstheendofthe
longest, followed by the first, third and then second (i.e., a leg limb the tibia-metatarsus joint is a superior bicondylar hinge,
sequenceof4,1,3,2tousemodernspidernotation).Therearea
visible in NHM In 27756 (Fig. 1.16). In Palaeocharinus (and in
few exceptions, such as the family Anthracosironidae whose
anthracomartids) the metatarsus (or basitarsus in some terminol-
anterior legs are enlarged and raptorial. Leg four is often a little
ogies) is short and almost quadratic; although this podomere is
stouterthantherest.Withtheexceptionofthefemur(seebelow),
usually longer in other trigonotarbids. Study of Palaeocharinus
thelimbsortrigontarbidsexhibitlittlelateralflattening—theyare
also reveals almost lyriform groups of slit sensilla (Fig. 5): two
largely rectangular to circular in cross-section (Fig. 1.7). A
groupsofsixslitsparalleltothelongaxisofthepodomereonthe
general reconstruction of the walking leg in Palaeocharinus is
ventro-lateraldistalmetatarsus(NHMIn27756;seealsoDunlop
presented (Fig. 4).
andBraddy,1997,fig.4).Themetatarsus-tarsusjointisasuperior
The articulations reported here from the Rhynie Chert
monocondylarhinge(NHMIn27760,In27758).Thedistaltarsus
paleocharinids, differ in some aspects from those described by
bears a dorsal tubercle from which a small number of relatively
Shear et al. (1987) for trigonotarbids from the mid-Devonian of
longsetaeemerge(Fig.1.8),andapairoflargecurved,pretarsal
Gilboa. The leg coxae of Palaeocharinus, and some other
clawswithasmaller,downward-pointing,medial,empodialclaw
trigonotarbids, possess mesal endites whose function remains
(Fig. 1.11). These may have moved as a single unit, articulating
unclear(Garwood etal.,2009;see Discussion).Atpresent, there
against an antero-ventral pair of tarsal projections (NHM In
isnoevidenceformovablearticulationsatthebody-coxaejointof
27758). A single (?claw depressor) tendon can clearly be seen
the trigonotarbid walking legs. This is consistent with other
runningfromthebaseofthisclawunit(Fig.1.8).Interestinglyno
arachnids, in which the coxae are largely fixed and the principal
corresponding levator tendon is visible, as would be predicted
leg movement comes from the next articulation: the coxa-
fromthelegmusculatureofotherarachnids(Shultz,1989).Ifthis
trochanter. Details of this joint are largely equivocal in Palae-
tendonandmusclearegenuinelyabsent,thiscouldbeinterpreted
ocharinus, but in NHM In 24675 there are hints of at least a
asaputativetrigonotarbidapomorphyandraisesquestionsabout
dorsal articulation point (Dunlop, 1994b) consistent with the
how the claw unit was raised in life. Distal claws were
infero-anterior and supero-posterior articulation points (Fig. 1.2)
presumably present in non-paleocharinid trigonotarbids too, but
described in the Gilboa material (Shear et al., 1987). If correct, areonlyrarelypreserved(e.g.,Petrunkevitch,1949,fig.199)for
this would suggest a dorso-ventral bicondylar hinge. Palae- anthracomartids.
ocharinuspossessessphericaltrochantersonlegsonetothree,in Blender.—These results informed the limb motion of our
whichthereisaproximalprojectionwhichappearstoslotintothe Blender model, as outlined in the Blender methods section.
coxa (Fig. 1.11,1.15). By contrast, trochanter four is larger and Online Supplemental Data file 2 is a video, showing first the
ovalinshape.Thispatternisseeninothertrigonotarbidfamilies, flexingofthelimbsaccordingtothearticulationsreportedabove,
whose globose trochanters widen distally, and an oblique from a walking pose to under the body, and then back to their
articulation to the femur aids the radiation of the legs. Distal to formerposition.Subsequentlythevideoshowsthelikelywalking
this, the trochanter-femur articulation (best seen in NHM In gait for the trigonotarbids (see Discussion). Also presented are
24673)isclearlyahorizontalanterior-posteriorbicondylarhinge rendersofthemodel(Fig.6)atdifferentstagesofitswalkcycle,
with the center of mass (as estimated by Blender) marked.
(Fig. 1.10, 1.11). It expresses a narrow ring of cuticle (the
Blender files for both animations are provided as online
annulus),whichencirclesthetrochanter-femurjoint.Thefemuris
Supplemental Data files 3 and 4.
usually the longest and broadest podomere and demonstrates a
degree of lateral compression in some taxa.
DISCUSSION
The femur-patella joint is a superior bicondylar hinge, as seen Advantages and limitations of Blender, and comparisons to
in NHM In 24673 (Fig. 1.11) and In 27756 (Fig. 1.13, 1.14). other software.—Blender is published under a GNU General
Significantly, this joint lacks a ventral arcuate sclerite, an extra Public License. It is both freely available and under regular
cuticularelementembeddedintothearthrodialmembraneseenin development. Thus it has a number of strengths: it is free, and
spidersandtheextinctandspider-likeorderUraraneida(Seldenet possesses diverse capabilities typical of high-end (normally
742 JOURNAL OF PALEONTOLOGY, V. 88, NO. 4, 2014
FIGURE6—ThePalaeocharinusspp.modelcreatedinBlenderforthecurrentstudy.1–3,differentphasesofthewalkingcyclefromadorsalperspective,with
legmovementsmarked:1,3,opposingsetsoffourlimbsaremakingcontactwiththefloor;2,themidpointbetweenopposingstepsinthecycle;limbmotionis
markedwitharrows,thecenterofmasswitharedcross,andafour-sidedpolygondefinedbythefourlimbsincontactwiththesubstrateismarkedonwitha
dottedredline;thisdemonstratesthatthecenterofmassremainswithinthelinemadebythelegsonthegroundateverypointinthesteppingcycle;4,an
anterior-lateralviewofthemodelwithlegsinaweight-bearing,plantigradestance;5,thesameviewwithlegscurledbeneaththebody;6,ventralview;7,the
stepcyclefromalateralview,atequivalentto2;8,lateralviewoftheoppositepartofthestepcycle,mid-waybetweenthepositionshownin3and1.
expensive)3-Dsoftware.Furthermore,itiscapableofimporting/ articulations and comparison with modern spiders in the current
exporting a wide range of file formats, and modifying/animating work—should be presented. Although it has improved consider-
meshes in many ways—accordingly, it can be useful in data ably since Blender 2.4X, the Blender 2.5/2.6 graphical user
processing, as well as rendering finalized images and movies. interface (GUI), is custom-built, and is very different from a
There are, however, numerous limitations to the software: for typical GUI, making it feel, at times, rather counterintuitive. As
the vast majority of virtual paleontology applications, it requires withanypieceof3-Dsoftware,especiallyonesoversatile,there
data which have been processed on other software prior to is also a steep learning curve (which this guide is intended to
importing finalized meshes into Blender. Indeed, Blender is reduce). Nevertheless, many of the processing/creation capabil-
primarily a computer graphics package, and so allows the user itiesofBlendercanbefoundinothersoftware,andtheuserneeds
almost unlimited freedom when creating and animating models. toassesswhetherlearningthisprogramjustifiestheimprovement
The software is not comparable to analytical software (e.g., achieved in rendered image quality. A strong user community
SIMM;Hutchinsonetal.,2005).Thusjustificationforanatomical (blender.org), and a number of books intended to introduce the
and mechanical elements of Blender outputs—such as limb software (Hess, 2010) are also helpful in this regard. Some
GARWOOD AND DUNLOP—BLENDER, A UTILITY FOR PALEONTOLOGISTS 743
datasets(CTinparticular)tendtopossessstatisticalnoise(Sutton The legs of Palaeocharinus are generally better preserved and
et al. 2013), which creates models with ‘bumpy’ surfaces, and allowmoreinferencestobemade.Theextentofcoxalmobilityin
thusveryhightrianglecounts.Inthecurrentauthors’experience, life is hard to ascertain, but the projecting coxal endites in
Blender universally loads these, however, manipulations and anthracomartids(Garwoodetal.,2009)wouldonlyhaveallowed
rendering can be slow with large models. limited coxal movement, and the same was probably true of
There are a number of three-dimensional computer animation Palaeocharinus (e.g., Fayers et al., 2005). It is interesting to
suites comparable to Blender. These include 3ds Max, Autodesk speculatewhetherthesetoseandgranularmesalendites(Fig.1.5)
Maya,ZBrushandCinema4D,tonameafew,allofwhichdiffer onatleasttheanteriorlegcoxaeofPalaeocharinusareremnants
subtly in their focus and capabilities. Of these Autodesk Maya ofagnathobase-likeconditionwith(originally?)anactiverolein
(http://www.autodesk.com/products/autodesk-maya/overview) feeding. In a wider context, this may document an intermediate
hasarguablyacquiredthelargestfollowinginthepaleontological state in the shift from movable coxae with toothed gnathobases
community, albeit one which remains limited to a handful of andanactiveroleinfoodprocessinginanaquaticenvironment—
researchers (Sellers et al., 2009; Molnar et al., 2012; Pittman et as in the outgroups Xiphosura (horseshoe crabs) or Eurypterida
al., 2013). The software is available as a free 30-day trial (or, (sea scorpions)—to the largely fixed coxae of most arachnids
currently, a 3-yr free license for students), and the full package whichformasolid,ventralbasetotheprosomaagainstwhichthe
costs $3,675/£3,795. It differs from Blender in terms of its high rest of the legs can articulate when walking in the more
end capabilities: both packages have individual features unavail- biomechanically challenging conditions of a terrestrial environ-
able in the other. However, we believe that the capabilities of ment.
both extend far beyond the needs of the paleontological Lackofcoxalmobilityimpliesthat,asinRecentarachnids,the
community. Thus one of the few advantages of Autodesk Maya propulsive back stroke (remotor) and recovery forward stroke
is an arguably more intuitive user interface. However, for (promotor) action during walking derived primarily from the
inexperienced users, the learning curve remains steep. coxa-trochanter joint. The essentially dorso-ventral bicondylar
Animation.—Animating the Blender model required, in addi- hinge (Figs. 1.2, 4) inferred here would facilitate the anterior-
tion to the correct limb articulations outlined in the Results, an posteriormovementrequiredtomovethelegforwards.Notethat
assessmentofthelikelygait.ThewalkinglegsofPalaeocharinus insome extant arachnids, the coxa-trochanter joint isoften more
are fairly homogenous, all about the same length, and similar in complex, and can also allow a degree of levator-depressor
shape and articulation to the legs of many spiders; particularly movement (cf. Shultz, 1989, 1999). Such freedom of movement
thosewithafree-livingecologysuchastarantulasorwolfspiders, is,inpart,thankstothepresenceofso-calledintercalarysclerites
as opposed to web-builders which often have more elongate (orasinglescleriteinspiders)whichhavebeenreportedfromthe
forelimbs and slender legs in general (see Foelix, 2011 for an
coxa-trochanter articulation of the clade Tetrapulmonata (e.g.,
overview). The most likely gait—also seen in other arachnids
Shultz,1990):agroupcomprisingthespiders,whipspiders,whip
which employ an octopedal gait such as scorpions (Spagna and
scorpionsandschizomids.Suchscleriteshavenotbeenobserved
Peattie, 2012)—is thus an alternating tetrapod. Biancardi et al.
in any trigonotarbid to date, although their presence cannot be
(2011) demonstrated that the tarantula Grammostola mollicoma,
entirely ruled out. Drawing on the phylogenies of Shear et al.
employs two walking quadrupeds, with almost no phase delay
(1987) and Selden et al. (1991), Shultz (2007) recognized a
betweenthem(i.e.,analmostidealalternatingtetrapodgait).The
Pantetrapulmonata clade comprising (TrigonotarbidaþTetrapul-
same gait is used at high speeds in fast-moving spiders but in a
monata). If intercalary sclerites are indeed absent in trigonotar-
less rigid fashion. However, weshould cautionthat variability is
seen in many living taxa, both step-to-step and between step- bids this would imply 1) that these sclerites are apomorphic for
cycles(Wilson,1967;WardandHumphreys,1981;Spagnaetal., Tetrapulmonata only and 2) that the trigonotarbid condition is
2011).Forexample,atarantulawalkingslowlymaymoveitslegs plesiomorphic. Indeed a simple bicondylar articulation at this
one by one, in a somewhat wave-like sequence (JAD, personal joint has been scored as plesiomorphic for arachnids (Shultz,
observ.),andonlyswitchestothemoremechanical‘tetrapod’gait 1990;Pepatoetal.,2010).Furthermore,theapparentweaknessof
when running. Blender can display the center of mass of an thearticulationatthisjointiscoupledwithaproximalprojection
object,whichinthiscaseliesontheopisthosomalmacrotergite2 slotting into the coxa in this joint (Fig. 1.15), reminiscent of a
þ3,abouttwo-thirdsfromitsanteriormargin.Thispositionisin tubular‘ballandsocket’joint.Bothofthesefactorsmayindicate
agreement with the assumption that paleocharinids used an a relatively mobile articulation, albeit without strong condyles.
alternating tetrapod gait and Figure 6.1–6.3 demonstrate that A strong, horizontal bicondylar hinge at the trochanter-femur
throughout their walking cycle the center of mass would have jointsuggeststheprinciplelevator-depressormovementoftheleg
remainedwithinthequadrupedincontactwiththefloor,therefore probably originated here (Figs. 1.10, 4). The aforementioned
maintaining stability. For the videos presented herein (online annulusatthisjoint—acuticularringseeninboththeRhynieand
Supplemental Data file 2) Palaeocharinus was made to walk
Gilboa paleocharinids (Shear et al., 1987)—may have strength-
fairly briskly with an idealized alternating tetrapod gait—and
enedthenarrowproximalregionofthefemur.Thepresenceofan
slight corresponding movements of the pedipalps—although in
annulus in non-Devonian trigonotarbids remains equivocal. Note
life a more variable and wave-like stepping pattern may have
thatscleritesinthisjointmembraneareseeninbothmodernand
been adopted at low speeds.
fossil Amblypygi (Dunlop and Martill, 2002) and the annulus
Limb functional morphology.—Other than the distal claw, the
could be homologous with these sclerites given that trigonotar-
pedipalps of Palaeocharinus show relatively few specializations
bidsusuallyresolvebasaltothetetrapulmonates(seeabove).This
and were probably used primarily for prey capture and/or the
annulushasbeencomparedtothe‘doubletrochanter’or‘divided
subsequent manipulation of food. The granular endites on the
coxae might have played a role in mastication, similar to the femur’ in other arachnids, but the polarity of this character state
serrated serrula seen on the palpal coxae (‘maxillae’ in some remains poorly understood; see Shultz (1989, 2007) for further
terminologies) of the more derived labidognath spiders (Foelix, discussionofhomologyandthehypothesisofaseparatebasi-and
2011).Inspidersthese‘maxillae’areoftenquitemobileandcan telofemur in the arachnid ground pattern.
actively chew, but we can only speculate whether trigonotarbids While strong, the femur-patella joint in Palaeocharinus was
alsomasticatedpreyusingthepedipalpalcoxaeorsimplypressed likelytohavehadalowerdegreeofflexionthanispossibleatthe
food items against the raised granules. same‘knee’jointinspiders.Thearcuatescleriteontheunderside