Bioinformatics and Systematics of the Beetles
Sample Data
This project was incorporated into Biology 1108L, Principles of Biology 2, at Gainesville State
College (University of North Georgia) in Summer 2011 (2 sections) Spring 2012 (6 sections), and Fall
2012 (4 sections). This course focuses on organismal biology, including diversity, morphology, and
ecology. Biology 1107L, which covers cell biology, genetics, and evolution, is the pre-requisite. We
selected this as the first lab of the semester, to transition from the content of Biology 1107L.
Spring 2012 students had been taught phylogenies prior to Biology 1108L, while Summer 2011
students had not, due to a change in Biology 1107. In general, morphological characters selected by
students focused on color, patterns, antennal shape/length, thorax shape/length, and elytra shape/length
(Table 1). After careful character selection students were able to generate trees that generally followed
the character tables, and were able to avoid repeated convergent traits on their trees (Figure 1). These
trees often did not match accepted phylogenetic relationships.
Callosobruchus Dorcus titanus
maculatus
antennae
>1/2 body
exaggerated
mandibles
Olla v-nigrum
Hippodamia
parenthesis
Cryptolaemus
montrouzieri
+
-
-
-
-
-
+
-
-
-
spotted elytra
-
-
+
+
+
hairy
-
-
-
-
+
Table 1. A sample student-generated matrix of morphological characters, indicating presence and
absence of each character.
Figure 1. A sample student-generated phylogenetic tree, using morphological characters selected in
Table 1.
The COI FASTA sequences obtained by students were noticeably different from each other, but not in
a way they could align on their own. Sequences created using these sequences differed from both the
morphological trees and the accepted phylogenies of these beetles (Figure 2, Figure 3). The distance
scale, a scale that represents the number of differences between sequences (e.g. 0.1 means 10%
differences between two sequences), is also shown below the image.
GENBANK sequences as displayed in FASTA used for phylogenetic tree construction:
>gi|386926342|gb|AFJ49050.1| cytochrome oxidase subunit 1, partial (mitochondrion)
[Callosobruchus maculatus]
TLYFIFGAWAGMAGTSLSMLIRAELGNPGSLIGNDQIYNVIVTAHAFIMIFFMVMPIMIGGFGN
WLVPLMLGAPDMAFPRMNNMSFWLLPPSLTLLLMSSMVESGAGTGWTVYPPLAANIAHSGS
SVDLAIFSLHLAGISSILGAVNFITTVINMRPTGMKMDQMPLFSWAVTITATLLLLSLPVLAGAI
TMLLTDRNLNTSFFDPAGGGDPILCQHLF
>gi|257649953|emb|CAR65071.1| cytochrome oxidase sub-unit 1 [Cryptolaemus montrouzieri]
GMIGTSLSMLIRLELGTPSALIGNDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMIGAPD
MAFPRLNNMSFWLLPPALTLLIMSSIVESGAGTGWTVYPPLSSNLAHSGPSVDLAIFSLHLAGI
SSILGAINFITTILNMRPYLMTLEKMPLFVWSVLITAVLLLLSLPVLAGAITMLLTDRNINTSFFD
PAGGGDPILYQHL
>gi|32352220|dbj|BAC78603.1| cytochrome oxidase I [Dorcus titanus sika]
RMNNMSFWLLPPSLTFLLMSSMVESGAGTGWTVYPPLSSNIAHSGASVDLAIFSLHLAGISSIL
GAVNFITTVINMRATGITFDRMPLFVWAVALTALLLLLSLPVLAGAITMLLTDRNINTTFFDPA
GGGDPILYQHLFWFFGHP
>gi|328878086|gb|AEB53742.1| cytochrome oxidase subunit I [Hippodamia parenthesis]
TLYFLFGMWAGMVGTSLSILIRLELGTTSSLIGNDQIYNVIVTAHAFIMIFFMVMPIMIGGFGN
WLVPLMIGAPDMAFPRLNNMSFWLLPPALTLLMFSSMVEMGAGTGWTVYPPLSSNLAHNGP
SVDLVIFSLHLAGISSILGAVNFISTIMNMRPYGMSLDKTPLFVWSVLITAILLLLSLPVLAGAIT
MLLTDRNLNTSFFDPTGGGDPILYQHLF
>gi|283463967|gb|ADB22567.1| cytochrome oxidase subunit I [Olla vnigrum]
SLSILIRLELGTTSSLIGNDQIYNVIVTAHAFIMIFFMVMPIMIGGFGNWLVPLMIGAPDMAFPRL
NNMSFWLLPPALTLLIMSSLIEMGAGTGWTVYPPLSSNLAHNGPSVDLVIFSLHLAGISSILGA
VNFISTIMNMRPLGMNLDKTPLFVWSVLITAILLLLSLPVLAGAITMLLTDRNINTSFFDPTGGG
DPILYQHLF
Figure 2. Phylogenetic tree created from COI amino acid FASTA sequences, obtained for
Callosobruchus maculatus, Cryptolaemus montrouzieri, Dorcus titanus, Hippodamia convergens, and
Olla v. nigrum. This tree was created using Phylogeny.fr (Dereeper et al., 2008). The distance scale, a
scale that represents the number of differences between sequences (e.g. 0.1 means 10% differences
between two sequences), is shown below the image. The numbers in red are the bootstrap values, a
statistical measure of how consistently the data support the proposed branch (values range from 0.0 –
1.0).
Figure 3. Accepted phylogenetic relationship among Callosobruchus maculatus, Cryptolaemus
montrouzieri, Dorcus titanus, Hippodamia convergens, and Olla v. nigrum. Relationships were
inferred using the Tree of Life Project website, Polyphaga (Coleoptera) page, last updated 1995.
Literature Cited
Dereeper, A., Guignon, V., Blanc, G., Audic, S., Buffet, S., Chevenet, F., Dufayard, J.F., Guindon, S.,
Lefort, V., Lescot, M., Claverie, J.M. and Gascuel, O. 2008. Phylogeny.fr: robust phylogenetic
analysis for the non-specialist. Nucleic Acids Research Jul 1; 36 (Web Server Issue):W465-9. Epub
2008 Apr 19.
Tree of Life Project website, Polyphaga (Coleoptera) page, last updated 1995. www.tolweb.org
This experiment was written by Evan Lampert and Jennifer L. Mook, 2014 (www.beanbeetles.org).