Aims
Motivation
Intellectual Merit
Broader Impacts


AMNH
WTAMU
IBUNAM
CAS


Principal Investigators
Collaborators
Graduate Students
Undergraduate Students
High School Students
Technicians
Volunteers


Fieldwork
Museum Collections
Databasing and Mapping
Taxonomy
DNA Sequencing
Choice of Gene Loci
Laboratory Protocols

Phylogenetic Analysis
Publications/Authorship


Research Goals/Products
Training Program
Project Management

Choice of Gene Loci

Because alternative data sources are implicitly excluded when a particular data source (e.g., a particular set of morphological characters or a particular gene) is selected for a given study (Nixon & Carpenter 1996; Swofford et al. 1996), data source selection should be conducted on the basis of reasoned expectations of the value (in time and money) of the data (Nixon & Carpenter 1996). Regrettably, such decisions are seldom made. For example, although the choice of gene loci (genome samples of 500–1000 or more base-pairs that can be sequenced as single pieces in both directions) is a critical step in any molecular phylogenetic analysis, too many investigators make their selections on the basis of primers that are available and/or capable of amplifying the DNA of their study organisms, without regard for the phylogenetic utility of those loci at their level of interest (Brower & DeSalle 1994; Soltis & Soltis 1998).           
     It is generally accepted that more than one gene locus should be used for phylogenetic reconstruction and that at least one locus should be acquired from the recombinant nuclear genome (Avise 1989; Doyle 1992; Degnan 1993; Brower & DeSalle 1994; Brower et al. 1996; Maddison 1997; Doyle & Davis 1998).
     Six gene loci, collectively summing to ca. 5.6 kilobases, are being sequenced for all vaejovid species for this project. These loci were chosen not only because of the availability of primers that could consistently amplify sufficiently large, phylogenetically informative fragments, but also because they have been reported to evolve at different rates and would thus be expected to provide phylogenetic resolution at different, overlapping taxonomic levels (e.g., Simon et al. 1994; Wahlberg & Zimmermann 2000; Giribet et al. 2001b; Prendini et al. 2003).
     The three nuclear gene loci being sequenced are considered sufficiently conserved to be informative for resolving the major clades of Vaejovidae, testing monophyly of the vaejovid genera, placing the family in the broader context of scorpion phylogeny and testing the contentious hypothesis that Uroctonus is a chactid and not a basal vaejovid (Soleglad & Fet 2003, 2004). Complete sequence of the small-subunit ribosomal RNA gene (18S rDNA), a variable fragment (D3 region) of the large-subunit ribosomal RNA gene (28S rDNA), and a variable fragment of the Histone H3 protein-coding gene, are being amplified. These fragments have been used in various studies of arthropod phylogeny at higher and lower levels (e.g., Turbeville et al. 1991; Carmean et al. 1992; Wheeler et al. 1993a,b; Wheeler 1997, 1998a; Colgan et al.1998; Wheeler & Hayashi 1998; Zrzavý et al. 1998, 2001; Edgecombe et al. 1999, 2000; Giribet et al. 1999a,b, 2001b, 2002; Giribet & Ribera 2000; Wheeler et al. 2001; Prendini et al. 2003).
     In order to provide resolution among the terminal taxa, and within the vaejovid genera, three gene loci were selected from the more labile mitochondrial genome. Comparatively labile fragments of the mitochondrial homologs of the nuclear small-subunit ribosomal RNA gene (12S rDNA) and the nuclear large-subunit ribosomal RNA gene (16S rDNA), both of which also contain conserved regions, were chosen, together with a more conserved fragment of the Cytochrome c Oxidase subunit I (CO I) protein-coding gene. The 12S fragment has been used in studies of the internal relationships of arthropods, scorpions and insects (e.g., Ballard et al. 1992; Simon et al. 1994; Wägele & Stanjek 1995; Zrzavý et al. 1998; Prendini et al. 2003). The 16S fragment has been employed in studies of interspecific and intraspecific variation within insects (Xiong and Kocher 1991; Vogler & DeSalle 1993; Vogler et al. 1993a,b; Simon et al. 1994; Fang et al. 1995; Wahlberg & Zimmermann 2000; Zimmermann et al. 2000), scorpions (Gantenbein et al. 1999a,b, 2000a,b, 2001a,b; Scherabon et al. 2000; Fet et al. 2001; Prendini et al. 2003) and spiders (Arnedo et al. 2002), and was also recently used in studies of arthropod phylogeny (Zrzavý et al. 1998; Giribet et al. 2001b). The CO I fragment has been used to determine relationships within Coleoptera, Lepidoptera, Orthoptera and other insect groups (Harrison et al. 1987; Simon et al. 1994; Wahlberg & Zimmermann 2000; Zimmermann et al. 2000), as well as among spiders (Arnedo et al. 2002), scorpions (Prendini et al. 2003), and in a study of arthropod higher phylogeny (Giribet et al. 2001b).           
     The following additional loci, Elongation Factor 1-α and Polymerase II (nuclear genome) and NADH dehydrogenase subunit I and Cytochrome Oxidase II (mitochondrial genome), may be added to the existing sample if found to contain sufficient variation and be reasonably easy to amplify.

Literature Cited

Arnedo, M.A., Oromí, P. & Ribera, C. 2002. Radiation of the spider genus Dysdera (Araneae, Dysderidae) in the Canary Islands: Cladistic assessment based on multiple data sets. Cladistics 17: 313–353.

Avise, J.C. 1989. Gene trees and organismal histories: A phylogenetic approach to population biology. Evolution 43: 1192–1208.

Ballard, J.W.O., Ballard, O., Olsen, G.J., Faith, D.P., Odgers, W.A., Rowell, D.M. & Atkinson, P. 1992. Evidence from 12S ribosomal RNA sequences that onychophorans are modified arthropods. Science 258: 1345–1348.

Brower, A.V.Z. & DeSalle, R. 1994. Practical and theoretical considerations for choice of a DNA sequence region in insect molecular systematics, with a short review of published studies using nuclear gene regions. Annals of the Entomological Society of America 87: 702–716.

Brower, A.V.Z., DeSalle, R. & Vogler, A. 1996. Gene trees, species trees, and systematics: a cladistic perspective. Annual Review of Ecology and Systematics 27: 423–450.

Carmean, D., Kimsey, L.S. & Berbee, M.L. 1992. 18S rDNA sequences and the holometabolous insects. Molecular Phylogenetics and Evolution 1: 270–278.

Colgan, D.J., McLauchlan, A., Wilson, G.D.F., Livingston, S.P., Edgecombe, G.D., Macaranas, J., Cassis, G. & Gray, M. R. 1998. Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Australian Journal of Zoology 46: 419–437.

Degnan, S.D. 1993. The perils of single gene trees—mitochondrial versus single-copy nuclear DNA variation in white-eyes (Aves: Zosteropidae). Molecular Ecology 2: 219–225.

Doyle, J.J. 1992. Gene trees and species trees: Molecular systematics as one-character taxonomy. Systematic Botany 17: 144–163.

Doyle, J.J. & Davis, J.I. 1998. Homology in molecular phylogenetics: A parsimony perspective. In: Soltis, D.E., Soltis P.S. & Doyle, J.J. (Eds.) Molecular Systematics of Plants II: DNA Sequencing. Kluwer Academic Publishers, Dordrecht, 101–131.

Edgecombe, G.D., Giribet, G. & Wheeler, W.C. 1999. Filogenia de Chilopoda: Combinado secuencias de los genes ribosómicos 18S y 28S y morfología [Phylogeny of Chilopoda: Analysis of 18S and 28S rDNA sequences and morphology]. In: Melic, A., De Haro, J.J., Mendez, M. & Ribera, I. (Eds.) Evolución y Filogenia de Arthropoda. Boletin de la Sociedad Entomología Aragonesa 26: 293–331.

Edgecombe, G.D., Wilson, G.D.F, Colgan, D.J., Grey, M.R. & Cassis, G. 2000. Arthropod cladistics: Combined analysis of histone H3 and U2 snRNA sequences and morphology. Cladistics 16: 155–203.

Fang, Q., Blocker, H.D. & Black, W.C., IV. 1995. Cladistic analysis of Nearctic Deltocephalus-like leafhoppers (Homoptera: Cicadellidae) using morphological and molecular data. Annals of the Entomological Society of America 88: 316–323.

Fet, V. & Selden, P.A. (Eds.) 2001. Scorpions 2001. In Memoriam Gary A. Polis. British Arachnological Society, Burnham Beeches, Buckinghamshire, UK.

Gantenbein, B., Fet, V. & Barker, M.D. 2001a. Mitochondrial DNA reveals a deep, divergent phylogeny in Centruroides exilicauda (Wood, 1863) (Scorpiones: Buthidae). In: Fet, V. & Selden, P.A. (Eds.) Scorpions 2001. In Memoriam Gary A. Polis. British Arachnological Society, Burnham Beeches, Bucks, UK, 235–244.

Gantenbein, B., Fet, V., Barker, M. & Scholl, A. 2000a. Nuclear and mitochondrial markers reveal the existence of two parapatric scorpion species in the Alps: Euscorpius germanus (C. L. Koch, 1837) and E. alpha Caporiacco, 1950, stat. nov. (Euscorpiidae). Revue suisse de Zoologie 107: 843–869.

Gantenbein, B., Fet, V., Largiadèr, C.R. & Scholl, A. 1999a. First DNA phylogeny of Euscorpius Thorell, 1876 (Scorpiones, Euscorpiidae) and its bearing on taxonomy and biogeographic of this genus. Biogeographica 75: 49–65.

Gantenbein, B., Kropf, C., Largiadèr, C. R. & Scholl, A., 2000b. Molecular and morphological evidence for the presence of a new buthid taxon (Scorpiones: Buthidae) on the island of Cyprus. Revue suisse de Zoologie 107: 213–232.

Gantenbein, B., Largiadèr, C.R. & Scholl, A. 1999b. Nuclear and mitochondrial gene variation of Buthus occitanus (Amoreux, 1789) across the Strait of Gibraltar. Revue suisse de Zoologie 104: 760.

Gantenbein, B., Soleglad, M. E. & Fet, V., 2001b. Euscorpius balearicus Caporiacco, 1950, stat. nov. (Scorpiones: Euscorpiidae): molecular (allozymes and mtDNA) and morphological evidence for an endemic Balearic Islands species. Organisms, Diversity and Evolution 1: 301–320.

Giribet, G. & Ribera, C. 2000. A review of arthropod phylogeny: New data based on ribosomal DNA sequences and direct character optimization. Cladistics 16: 204–231.

Giribet, G., Carranza, S., Riutort, M., Baguñà, J. & Ribera, C. 1999b. Internal phylogeny of the Chilopoda (Myriapoda, Arthropoda) using complete 18S rDNA and partial 28S rDNA sequences. Philosophical Transactions of the Royal Society of London B 354: 215–222.

Giribet, G., Edgecombe, G.D. & Wheeler, W.C. 2001b. Arthropod phylogeny based on eight molecular loci and morphology. Nature 413: 157–161.

Giribet, G., Edgecombe, G.D., Wheeler, W.C. & Babbitt, C. 2002. Phylogeny and systematic position of Opiliones: A combined analysis of chelicerate relationships using morphological and molecular data. Cladistics 18: 5–70.

Giribet, G., Rambla, M., Carranza, S., Riutort, M., Baguñà, J. & Ribera, C. 1999a. Phylogeny of the arachnid order Opiliones (Arthropoda) inferred from a combined approach of complete 18S, partial 28S ribosomal DNA sequences and morphology. Molecular Phylogenetics and Evolution 11: 296–307.

Harrison, R.G., Rand, D.M. & Wheeler, W.C. 1987. Mitochondrial DNA variation in field crickets across a narrow hybrid zone. Molecular Biology and Evolution 24: 363–371.

Maddison, W.P. 1997. Gene trees and species trees. Systematic Biology 46: 523–536.

Nixon, K.C. & Carpenter, J.M. 1996. On simultaneous analysis. Cladistics 12: 221–241.

Prendini, L., Crowe, T.M. & Wheeler, W.C. 2003. Systematics and biogeography of the family Scorpionidae Latreille, with a discussion of phylogenetic methods. Invertebrate Systematics 17: 185–259.

Scherabon, B., Gantenbein, B., Fet, V., Barker, M., Kuntner, M., Kropf, C. & Huber, D. 2000. A new species of scorpion for Austria, Italy, Slovenia and Croatia: Euscorpius gamma Caporiacco, 1950, stat. nov. (Scorpiones, Euscorpiidae). Ekólogia (Bratislava) 19: 253–262.

Simon, C., Frati, F., Beckenbach, A., Crespi, B., Liu, H. & Flook, P. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Annals of the Entomological Society of America 87: 651–701.

Soleglad, M.E. & Fet, V. 2003. High-level systematics and phylogeny of the extant scorpions (Scorpiones: Orthosterni). Euscorpius 11: 1–175.

Soleglad, M.E. & Fet, V. 2004. The systematics of the scorpion subfamily Uroctoninae (Scorpiones: Chactidae). Revista Ibérica de Aracnología 10: 81–128.

Soltis, D.E. & Soltis, P.S. 1998. Choosing an approach and an appropriate gene for phylogenetic analysis. In: Soltis, D.E., Soltis, P.S. & Doyle, J.J. (Eds.) Molecular Systematics of Plants II: DNA Sequencing. Kluwer Academic Publishers, Dordrecht, 1–42.

Swofford, D.L., Olsen, G.J., Waddell, P.J. & Hillis, D.M. 1996. Phylogenetic inference. In:  Hillis, D.M., Moritz C. & Mable, B.K. (Eds.) Molecular Systematics. 2^nd edition. Sinauer Associates: Sunderland, MA, 407–514.

Turbeville, J.M., Pfeifer, D.W., Field, K.G. & Raff, R.A. 1991. The phylogenetic status of arthropods, as inferred from 18S rRNA sequences. Molecular Biology and Evolution 8: 669–686.

Vogler, A.P. & DeSalle, R. 1993. Phylogeographic patterns in coastal North American tiger beetles, Cicindela dorsalis, inferred from mitochondrial DNA sequences. Evolution 47: 1192–1202.

Vogler, A.P., DeSalle, R., Assmann, T., Knisley, C.B. & Schultz, T.D. 1993a. Molecular population genetics of the endangered tiger beetle Cicindela dorsalis (Coleoptera: Cicidelidae). Annals of the Entomological Society of America 86: 142–152.

Vogler, A.P., Knisley, C.B., Glueck, S.B., Hill, J.M. & DeSalle, R. 1993b. Using molecular and ecological data to diagnose endangered populations of the puritan tiger beetle Cicindela puritans. Molecular Ecology 2: 375–383.

Wägele, J.W. & Stanjek, G. 1995. Arthropod phylogeny inferred from partial 12S rRNA revisited: Monophyly of the Tracheata depends on sequence alignment. Journal of Zoological Systematics and Evolution Research 33: 75–80.

Wahlberg, N. & Zimmermann, M. 2000. Pattern of phylogenetic relationships among members of the tribe Melitaeini (Lepidoptera: Nymphalidae). Cladistics 16: 347–363.

Wheeler, W.C. 1997. Sampling, groundplans, total evidence and the systematics of arthropods. In: Fortey, R.A. & Thomas, R.H. (Eds.) Arthropod Relationships. Systematics Association Special Publications Vol. 55. Chapman & Hall, London, 87–95.

Wheeler, W.C. 1998. Molecular systematics and arthropods. In: Edgecombe, G.E. (Ed.) Arthropod Fossils and Phylogeny. Columbia University Press, New York, 9–32.

Wheeler, W.C. & Hayashi, C.Y. 1998. The phylogeny of extant chelicerate orders. Cladistics 14: 173–192.

Wheeler, W.C., Cartwright, P. & Hayashi, C. 1993a. Arthropod phylogeny: A combined approach. Cladistics 9: 1–39.

Wheeler, W.C., Schuh, R.T. & Bang, R. 1993b. Cladistic relationships among higher groups of Heteroptera: Congruence between morphological and molecular data sets. Entomologica scandinavica 24: 121–137.

Wheeler, W.C., Whiting, M., Wheeler, Q.D. & Carpenter, J.M. 2001. The phylogeny of the extant Hexapod orders. Cladistics 17: 113–169.

Xiong, B. & Kocher, T. D., 1991. Comparison of mitochondrial DNA sequences of seven morphospecies of black flies (Diptera: Simuliidae). Genome 34: 306–311.

Zimmermann, M., Wahlberg, N. & Descimon, H., 2000. Phylogeny of Euphydryas checkspot butterflies (Lepidoptera: Nymphalidae) based on mitochondrial DNA sequence data. Annals of the Entomological Society of America 93: 347–355.

Zrzavý, J., Hypša, V. & Tietz, D. F., 2001. Myzostomida are not annelids: Molecular and morphological support for a clade of animals with anterior sperm flagella. Cladistics 17: 170–198.

Zrzavý, J., Hypša, V. & Vlášková, M., 1998. Arthropod phylogeny: Taxonomic congruence, total evidence and conditional combination approaches to morphological and molecular data sets. In: Fortey, R.A. & Thomas, R.H. (Eds.) Arthropod Relationships. Systematics Association Special Publications Vol. 55. Chapman & Hall, London, 97–107.