DOI: 10.5061/dryad.v41ns1s2t
title: Raw data and Matlab code for: Convergence in carnivorous pitcher plants reveals a mechanism for composite trait evolution

description: Composite traits involve multiple components that, only when combined,
 gain a new synergistic function. Thus, how they evolve remains a puzzle.
 We combined field experiments, microscopy, chemical analyses and laser
 Doppler vibrometry with comparative phylogenetic analyses to show that two
 carnivorous Nepenthes pitcher plant species convergently evolved identical
 adaptations in three distinct traits to acquire a new, composite trapping
 mechanism. Comparative analyses suggest that this new trait arose
 convergently via ‘spontaneous coincidence’ of the required trait
 combination, rather than directional selection in the component traits.
 Our results indicate a plausible mechanism for composite trait evolution
 and highlight the importance of stochastic phenotypic variation as a
 facilitator of evolutionary novelty.
description: Data were collected from 55 <em>Nepenthes
 </em>pitcher plant species from Botanical collections in the UK,
 Germany and Switzerland, as well as from two species (<em>N.
 gracilis</em> and <em>N. pervillei</em>) from natural
 populations in Borneo and the Seychelles. Fotos and high-speed videos were
 used to assess two macromorphological traits: (1) lid orientation
 (deviation from horizontal in °), and (2) lid loading/impact response
 (qualitatively from Fotos, and quantitatively from high-speed video
 recordings). Laser Doppler vibrometry was used for detailed analysis of
 lid oscillations after a drop impact on the lid. Scanning electron
 microscopy was used to assess surface microtopography (images are shown in
 the article supplementary material, Figures S1 and S2, and are not
 included in this dataset). Gas-chromatography mass-spectrometry was used
 to investigate the chemical composition of surface waxes. For detailed
 descriptions of the experimental methods and sampling techniques see
 online supplementary material, Materials and Methods.
description: No specialist software is required. Data files are in .csv
 format. Images are in .tif format. Video files are in .avi
 format.
description: **Data for: "Convergence in carnivorous pitcher plants reveals
 mechanism for composite trait evolution"** by Guillaume Chomicki,
 Gustavo Burin, Lucas Busta, Jedrzej Gozdzik, Reinhard Jetter, Beth
 Mortimer, Ulrike Bauer **Abstract:** The evolution of complex, composite
 traits remains a puzzle. Composite traits involve multiple components
 that, only when combined, gain a new synergistic function. Using field
 experiments, microscopy, chemical analyses, and laser Doppler vibrometry,
 we show that two carnivorous Nepenthes pitcher plants independently
 evolved identical adaptations in three distinct traits to acquire a new,
 complex trapping mechanism. Comparative phylogenetic analysis revealed
 that this composite trait arose convergently via spontaneous coincidence
 of independently evolving components with high pre-existing phenotypic
 variation, rather than gradual directional selection in one or more
 component traits. We show that high pre-existing phenotypic variability
 can generate evolutionary novelty by increasing the chance of a
 spontaneous beneficial combination of previously non-functional traits.
 *** <br> **Summary description:** Data were collected from 55
 Nepenthes pitcher plant species from Botanical collections in the UK,
 Germany and Switzerland, as well as from two species (N. gracilis and N.
 pervillei) from natural populations in Borneo and the Seychelles. Fotos
 and high-speed videos were used to assess two macromorphological traits:
 (1) lid orientation (deviation from horizontal in °), and (2) lid
 loading/impact response (qualitatively from Fotos, and quantitatively from
 high-speed video recordings). Laser Doppler vibrometry was used for
 detailed analysis of lid oscillations after a drop impact on the lid.
 Scanning electron microscopy was used to assess surface microtopography
 (images are shown in the article supplementary material, Figures S1 and
 S2, and are not included in this dataset). Gas-chromatography
 mass-spectrometry was used to investigate the chemical composition of
 surface waxes. For detailed descriptions of the experimental methods and
 sampling techniques see online supplementary material, Materials and
 Methods. *** <br> **Files (alphabetical):**
 ***Comparative\_dataset\_55species\_summary.csv*** Context: Testing the
 independent origin of springboard trapping; Testing for correlated
 evolution of the component traits of springboard trapping; Figs.3, S3-S7.
 Summary of the semi-quantitative trait data used to probe the evolutionary
 independence of springboard trapping in its three component traits in N.
 gracilis and N. pervillei. Data table. Rows: (1) header; (2-56) data.
 Columns: (A) species names; (B-G) qualitative load responses determined
 from manual loading of the lid tip (see online supplementary material,
 Materials and Methods, section Assessment of lid position and loading
 response); (B) number of individual pitchers showing a lid pivoting
 response; (C) number of individual pitchers showing a pivot-like response;
 (D) number of individual pitchers showing a lid bending response; (E)
 number of individual pitchers showing a lid buckling response; (F) number
 of individual pitchers showing a mixed bending-buckling response; (G)
 number of individual pitchers showing a complex mixture of response types,
 e.g. bending-buckling-twisting or pivoting-buckling; (H) sample sizes for
 each species; (I-K) three-state coding of lid loading responses for the
 ancestral state reconstructions and tests of independent evolution (see
 online supplementary material, Materials and Methods, section Testing the
 independent origins of springboard trapping); (I) equals (B); (J) equals
 (C); (K) equals SUM(D:G); (L-Q) proportion of each loading response
 category in percent; (L) proportion of pivoting lids in percent; (M)
 proportion of pivot-like lids in percent; (N) proportion of bending lids
 in percent; (O) proportion of buckling lids in percent; (P) proportion of
 bending-buckling lids in percent; (Q) proportion of complex response lids
 in percent; (R) predominant response (shown by &gt;50% of all
 investigated pitchers per species); if no single category reached 50%
 prevalence, the predominant response is ‘variable’; (S) predominant
 response using three-state coding: pivot = &gt;50% pivoting,
 pivot-like = &gt;50% pivoting OR pivot-like, non-pivot = pivoting +
 pivot-like &lt; 50%; (T) mean lid angle (°) = deviation from
 horizontal (see online supplementary material, Materials and Methods,
 section Assessment of lid position and loading response) for each species;
 (U) three-state coding of lid orientation for the ancestral state
 reconstructions and tests of independent evolution (see online
 supplementary material, Materials and Methods, section Testing the
 independent origins of springboard trapping): horizontal = ± 10° deviation
 from horizontal, near-horizontal = ± 20° deviation from horizontal,
 non-horizontal = &gt; ± 20° deviation from horizontal; (V) Three-state
 coding of wax crystal presence: wax = pillar-shaped wax crystals on the
 lower lid surface, weak wax = sparse or patchy wax crystals of variable
 shape, no wax = smooth lower lid surface, devoid of crystals; (W) Plant
 source (botanical collection), multiple sources are separated by commas.
 ***Custom\_matlab\_script\_for\_laser\_Doppler\_vibrometry.txt*** Context:
 Laser Doppler vibrometry of impact-induced lid oscillations; Fig.1, F and
 L. Matlab code used to analyze the laser Doppler vibrometry data (included
 as \*.csv files)
 ***Custom\_matlab\_script\_for\_tracking\_lid\_movement.txt*** Context:
 High-speed videography of the impact response of the pitcher lid; Fig.1, E
 and K. Matlab code used to track the lid movement in highspeed video files
 (included as \*.avi files)
 ***Highspeed\_video\_analysis\_mass\_area\_frequency.csv*** Context:
 High-speed videography of the impact response of the pitcher lid; Fig.1, E
 and K. Masses, areas and resonant frequencies of N. gracilis and N.
 pervilei lids tracked in highspeed videos (included as \*.avi files). Area
 determined from included \*tif files. Data table. Rows: (1) header; (2-17)
 data. Columns: (A) species; (B) pitcher identifier; (C) oscillation
 frequency of a tracked point near the lid attachment point (lid base), in
 s-1; (D) oscillation frequency of a tracked point halfway between lid
 attachment and distal lid tip (midpoint), in s-1; (E) oscillation
 frequency of a tracked point near the distal lid tip (tip), in s-1; (F)
 fresh lid mass in mg; (G) lid area in mm2; (H) mean oscillation frequency
 in (averaged over the frequencies in rows B-D), in s-1; see also online
 supplementary material, Materials and Methods, section High-speed
 videography of the impact response of the pitcher lid.
 ***Laser\_Doppler\_vibrometry\_data\_N\_gracilis.csv*** Context: Laser
 Doppler vibrometry of impact-induced lid oscillations; Fig.1, F and L. Raw
 data for 3 N. gracilis lids. Data table. Rows: (1) header; (2-4800) data.
 Columns: (A,C,E) time steps normalized for 5 oscillation cycles
 (dimensionless); (B,D,F) velocity normalized for lid size (dimensionless);
 (A,B) data for pitcher 3; (C,D) data for pitcher 2; (E,F) data for pitcher
 1; see also online supplementary material, Materials and Methods, section
 Laser Doppler vibrometry of impact-induced lid oscillations.
 ***Laser\_Doppler\_vibrometry\_data\_N\_pervillei.csv*** Context: Laser
 Doppler vibrometry of impact-induced lid oscillations; Fig.1, F and L. Raw
 data for 4 N. pervillei lids. Data table. Rows: (1) header; (2-4800) data.
 Columns: (A,C,E,G) time steps normalized for 5 oscillation cycles
 (dimensionless); (B,D,F,H) velocity normalized for lid size
 (dimensionless); (A,B) data for pitcher 7; (C,D) data for pitcher 5; (E,F)
 data for pitcher 6; (G,H) data for pitcher 4; see also online
 supplementary material, Materials and Methods, section Laser Doppler
 vibrometry of impact-induced lid oscillations.
 ***Laser\_Doppler\_vibrometry\_mass\_area\_frequency.csv*** Context: Laser
 Doppler vibrometry of impact-induced lid oscillations; Fig.1, F and L.
 Masses, areas and resonant frequencies of N. gracilis and N. pervilei lids
 investigated using laser Doppler vibrometry. Data table. Rows: (1) header;
 (2-8) data. Columns: (A) species; (B) pitcher identifier; (C) fresh lid
 mass (mg); (D) lid area (mm²); (E) lid oscillation frequency measured with
 a laser Doppler vibrometer, in s-1; see also online supplementary
 material, Materials and Methods, section Laser Doppler vibrometry of
 impact-induced lid oscillations. ***Lid\_angles\_raw\_data.csv*** Context:
 Testing the independent origin of springboard trapping; Testing for
 correlated evolution of the component traits of springboard trapping;
 Quantification of variation in lid angles and lid loading behavior in 42
 Nepenthes species; Figs.3, 5, S3-S8. Data table. Rows: (1) header; (2-74)
 data: angle measurements in (°). Columns (A-CK): Nepenthes species.
 ***Lid\_loading\_response\_raw\_data.csv*** Context: Testing the
 independent origin of springboard trapping; Testing for correlated
 evolution of the component traits of springboard trapping; Quantification
 of variation in lid angles and lid loading behavior in 42 Nepenthes
 species; Figs.3-5, S3-S9. Data table. Rows: (1) header; (2-77) data:
 qualitative load responses determined from manual loading of the lid tip
 (see online supplementary material, Materials and Methods, section
 Assessment of lid position and loading response). Columns (A-CK):
 Nepenthes species ***Lid\_wax\_raw\_data.csv*** Context: Testing the
 independent origin of springboard trapping; Testing for correlated
 evolution of the component traits of springboard trapping; Figs.3, 5,
 S1-S7. Data table. Rows: (1-86): data. Columns: (A) Nepenthes species
 names; (B) description of wax crystal presence and morphology as
 determined from scanning electron micrographs (one image per species; see
 also online supplementary material, Materials and Methods, section
 Scanning electron microscopy of lower lid surfaces)
 ***N\_gracilis\_lid\_area\_P02.tif***
 ***N\_gracilis\_lid\_area\_P05.tif***
 ***N\_gracilis\_lid\_area\_P06.tif***
 ***N\_gracilis\_lid\_area\_P07.tif***
 ***N\_gracilis\_lid\_area\_P08.tif***
 ***N\_gracilis\_lid\_area\_P09.tif***
 ***N\_gracilis\_lid\_area\_P10.tif***
 ***N\_gracilis\_lid\_area\_P11.tif***
 ***N\_gracilis\_lid\_area\_P12.tif***
 ***N\_gracilis\_lid\_area\_P13.tif***
 ***N\_gracilis\_lid\_area\_P14.tif*** Context: High-speed videography of
 the impact response of the pitcher lid; Fig.1E. Photographs of abscised N.
 gracilis lids on graph paper. Numbers in the file name identify individual
 pitchers. Image files. ***N\_gracilis\_P02-1.avi***
 ***N\_gracilis\_P02-2.avi*** ***N\_gracilis\_P02-3.avi***
 ***N\_gracilis\_P05-1.avi*** ***N\_gracilis\_P05-2.avi***
 ***N\_gracilis\_P05-3.avi*** ***N\_gracilis\_P06-1.avi***
 ***N\_gracilis\_P06-2.avi*** ***N\_gracilis\_P06-3.avi***
 ***N\_gracilis\_P07-1.avi*** ***N\_gracilis\_P07-2.avi***
 ***N\_gracilis\_P07-3.avi*** ***N\_gracilis\_P08-1.avi***
 ***N\_gracilis\_P08-2.avi*** ***N\_gracilis\_P08-3.avi***
 ***N\_gracilis\_P09-1.avi*** ***N\_gracilis\_P09-2.avi***
 ***N\_gracilis\_P09-3.avi*** ***N\_gracilis\_P10-1.avi***
 ***N\_gracilis\_P10-2.avi*** ***N\_gracilis\_P10-3.avi***
 ***N\_gracilis\_P11-1.avi*** ***N\_gracilis\_P11-2.avi***
 ***N\_gracilis\_P11-3.avi*** ***N\_gracilis\_P12-1.avi***
 ***N\_gracilis\_P12-2.avi*** ***N\_gracilis\_P12-3.avi***
 ***N\_gracilis\_P13-1.avi*** ***N\_gracilis\_P13-2.avi***
 ***N\_gracilis\_P13-3.avi*** ***N\_gracilis\_P14-1.avi***
 ***N\_gracilis\_P14-2.avi*** ***N\_gracilis\_P14-3.avi*** Context:
 High-speed videography of the impact response of the pitcher lid; Fig.1E.
 Highspeed video recordings of simulated rain drop impacts on N. gracilis
 lids. Numbers P02 to P14 identify individual pitchers. Numbers -1 to -3
 identify repeated drop impacts on the same lid. Video files.
 ***N\_pervillei\_lid\_area\_P06.TIF***
 ***N\_pervillei\_lid\_area\_P07.TIF***
 ***N\_pervillei\_lid\_area\_P08.TIF***
 ***N\_pervillei\_lid\_area\_P09.TIF***
 ***N\_pervillei\_lid\_area\_P10.TIF*** Context: High-speed videography of
 the impact response of the pitcher lid; Fig.1K. Photographs of abscised N.
 pervillei lids on graph paper. Numbers in the file name identify
 individual pitchers. Image files. ***N\_pervillei\_P06-1.avi***
 ***N\_pervillei\_P06-2.avi*** ***N\_pervillei\_P06-3.avi***
 ***N\_pervillei\_P06-4.avi*** ***N\_pervillei\_P06-5.avi***
 ***N\_pervillei\_P07-1.avi*** ***N\_pervillei\_P07-2.avi***
 ***N\_pervillei\_P07-3.avi*** ***N\_pervillei\_P07-4.avi***
 ***N\_pervillei\_P07-5.avi*** ***N\_pervillei\_P08-1.avi***
 ***N\_pervillei\_P08-2.avi*** ***N\_pervillei\_P08-3.avi***
 ***N\_pervillei\_P08-4.avi*** ***N\_pervillei\_P08-5.avi***
 ***N\_pervillei\_P09-1.avi*** ***N\_pervillei\_P09-2.avi***
 ***N\_pervillei\_P09-3.avi*** ***N\_pervillei\_P09-4.avi***
 ***N\_pervillei\_P09-5.avi*** ***N\_pervillei\_P10-1.avi***
 ***N\_pervillei\_P10-2.avi*** ***N\_pervillei\_P10-3.avi***
 ***N\_pervillei\_P10-4.avi*** ***N\_pervillei\_P10-5.avi*** Context:
 High-speed videography of the impact response of the pitcher lid; Fig.1K.
 Highspeed video recordings of simulated rain drop impacts on N. pervillei
 lids. Numbers P06 to P10 identify individual pitchers. Numbers -1 to -5
 identify repeated drop impacts on the same lid. Video files.
 ***Nepenthes\_wax\_GC-MS\_data.csv*** Context: Chemical analysis of
 surface waxes; Fig.2. Data table. Rows: (1) header; (2-197) data. Columns:
 (A) species name; (B) pitcher surface; (C) carbon-chain length of the
 identified wax compound; (D) compound class; (E) compound identifier; (F)
 compound abundance in µg cm^2, replicate sample 1; (G) compound abundance
 in µg cm^2, replicate sample 2; (H) compound abundance in µg cm^2,
 replicate sample 3; (I) compound abundance in µg cm^2, replicate sample 4.
 ***Trait\_variability\_dataset\_42species\_summary.csv*** Context:
 Quantification of variation in lid angles and lid loading behavior in 42
 Nepenthes species; Figs. 3-5, S8-9. Data table. Rows: (1) header; (3-44)
 data. Columns: (A) Nepenthes species; (B-H) lid angle measurements (see
 online supplementary material, Materials and Methods, section Assessment
 of lid position and loading response); (B) sample size; (C) mean lid angle
 (°); (D) standard error of the mean (±°); (E) median lid angle (°); (F)
 minimum lid angle (°); (G) maximum lid angle (°); (H) normal distribution
 of data (determined from Shapiro-Wilks tests if n ≤ 10 and
 Kolmogoroff-Smirnov tests if n &gt; 10), Y = yes, N = no; (I-AC)
 qualitative load responses determined from manual loading of the lid tip
 (see online supplementary material, Materials and Methods, section
 Assessment of lid position and loading response); (I) number of individual
 pitchers showing a lid pivoting response; (J) number of individual
 pitchers showing a pivot-like response; (K) number of individual pitchers
 showing a lid bending response; (L) number of individual pitchers showing
 a lid buckling response; (M) number of individual pitchers showing a mixed
 bending-buckling response; (N) number of individual pitchers showing a
 complex mixture of response types, e.g. bending-buckling-twisting or
 pivoting-buckling; (O) sample size; (P) average number of pitchers per lid
 loading category (= expected number per category under equal
 distribution); (Q) variance of data distribution across categories; (R)
 index of dispersion (variance-to-mean ratio); this is 1 for a perfectly
 random distribution, &lt;1 for an equal distribution, and &gt;1
 for an aggregated (clumped) distribution; (S) chi-square statistics for
 the index of dispersion; (T) degrees of freedom for the chi-square
 statistics; (U) data distribution determined from chi-square statistics
 with an error probability of &lt;5%; (V) data distribution determined
 from chi-square statistics with an error probability of &lt;1%; (W)
 proportion of pivoting lids in percent; (X) proportion of pivot-like lids
 in percent; (Y) proportion of bending lids in percent; (Z) proportion of
 buckling lids in percent; (AA) proportion of bending-buckling lids in
 percent; (AB) proportion of complex response lids in percent; (AC)
 predominant response (shown by &gt;50% of all investigated pitchers
 per species); if no single category reached 50% prevalence, the
 predominant response is ‘variable’ The code used for the corHMM analysis
 can be found at
 [https://github.com/gburin/nepenthes-springboard](https://github.com/gburin/nepenthes-springboard).