Considering Evolutionary Processes in the Use of Single-Locus Genetic Data for Conservation, with Examples from the Lepidoptera
Total Page：16
File Type：pdf, Size：1020Kb
J Insect Conserv (2008) 12:37–51 DOI 10.1007/s10841-006-9061-6 Considering evolutionary processes in the use of single-locus genetic data for conservation, with examples from the Lepidoptera Matthew L. Forister Æ Chris C. Nice Æ James A. Fordyce Æ Zachariah Gompert Æ Arthur M. Shapiro Received: 9 October 2006 / Accepted: 4 December 2006 / Published online: 1 February 2007 Ó Springer Science+Business Media B.V. 2007 Abstract The increasing popularity of molecular scale that is often much more rapid than the rates of taxonomy will undoubtedly have a major impact on mutation and allele frequency changes due to genetic the practice of conservation biology. The appeal of drift, neutral genetic variation at a single locus can be such approaches is undeniable since they will clearly a poor predictor of adaptive variation within or be an asset in rapid biological assessments of poorly among species. Furthermore, reticulate processes, known taxa or unexplored areas, and for discovery of such as introgressive hybridization, may also constrain cryptic biodiversity. However, as an approach for the utility of molecular taxonomy to accurately detect diagnosing units for conservation, some caution is significant units for conservation. A survey of pub- warranted. The essential issue is that mitochondrial lished genetic data from the Lepidoptera indicates DNA variation is unlikely to be causally related to, that these problems may be more prevalent than and thus correlated with, ecologically important previously suspected. Molecular approaches must be components of fitness. This is true for DNA barcod- used with caution for conservation genetics which is ing, molecular taxonomy in general, or any technique best accomplished using large sample sizes over that relies on variation at a single, presumed neutral extensive geography in addition to data from multiple locus. Given that natural selection operates on a time loci. Keywords DNA barcoding Á Molecular taxonomy Á Matthew L. Forister, Chris C. Nice and James A. Fordyce COI Á Lineage sorting Á Hybridization contributed equally to this paper. & M. L. Forister ( ) Introduction Department of Natural Resources and Environmental Science, University of Nevada, Mail Stop 186, 1000 Valley Road, Reno, NV 89512, USA A fundamental challenge for conservation biology is to e-mail: mforister@cabnr.unr.edu accurately identify units of biodiversity and to diagnose those units that merit conservation concern (Vane- C. C. Nice Á Z. Gompert Department of Biology, Population and Conservation Wright et al. 1991; Moritz 1994, 2002; Vogler and Biology Program, Texas State University, San Marcos, TX DeSalle 1994; Bowen 1998, 1999; Haig 1998; Grady and 78666, USA Quattro 1999; Paetkau 1999; Crandall et al. 2000; Goldstein et al. 2000; Fraser and Bernatchez 2001; J. A. Fordyce Department of Ecology and Evolutionary Biology, Agapow et al. 2004). Identification or circumscription University of Tennessee, Knoxville, TN 37996, USA of taxa consists of two different, yet equally important, aspects. First, identification can refer to the accurate A. M. Shapiro demarcation of a taxon previously described, such as a Section of Evolution and Ecology, Center for Population Biology, Storer Hall, University of California, Davis, CA species or population with a known conservation sta- 95616, USA tus. Second, identification can include the discovery of 123 38 J Insect Conserv (2008) 12:37–51 a new taxon and determination of whether it merits criticized the DNA barcoding agenda as being a conservation attention. Traditionally, identification has misapplication and simplification of molecular tech- been the responsibility of the taxonomist, who would niques (Sperling 2003a; Rubinoff 2006). Our concern often combine morphological, behavioral, life history, here is not with all of molecular phylogenetics, but ecological, and genetic data to determine taxon iden- with the utility of molecular taxonomic approaches tity. However, the number of taxonomic specialists, for demarcation, especially when they utilize single- those with an intimate knowledge of a group of locus genetic data (as emphasized by proponents of organisms, is declining. Funding for alpha taxonomy is DNA barcoding) and are applied to taxa of conser- increasingly scarce and even museums, the hearts of vation interest. What might the consequences be of taxonomy, are facing financial and philosophical chal- using DNA barcodes, or any single locus sequence, in lenges (Noss 1996; Wheeler 2004). Conversely, the field conservation? of molecular taxonomy (or molecular systematics) is Applying molecular taxonomy to conservation cer- growing in popularity. tainly has advantages for screening for illegal traffick- Molecular taxonomy uses genetic variation, usually ing of endangered species (Baker et al. 1996; DeSalle from one or more genes, to construct a phylogeny with and Birstein 1996; Palumbi and Cipriano 1998; Ludwig the implicit assumption that the gene genealogies re- 2006) and revealing cryptic species or lineages previ- flect the phylogeny of the species sampled (Pamilo and ously undescribed (e.g. Brower 1996; Omland et al. Nei 1988; Harrison 1989; Brower and DeSalle 1994; 2000; Witt et al. 2006; but see Irwin 2002) (for other Brower et al. 1996; Degnan and Rosenberg 2006). applications of phylogenetics in conservation see Pur- Molecular taxonomy has the advantage that it is rela- vis et al. 2005). However, the utility of phylogenetic tively easily applied, does not require the same approaches for identifying closely related taxa (par- expertise as traditional taxonomy, and, importantly, ticularly those of recent origin) or for diagnosing provides an evolutionary framework for the taxa in populations or lineages that merit protection is unre- question (Tautz et al. 2002, 2003). The pinnacle of solved (Sperling 2003a). The term evolutionary signif- enthusiasm for molecular approaches to taxonomy is icant unit (ESU) has been used to refer to populations DNA barcoding, which proposes the use of a 648 base or lineages that represent unique, significant adaptive pair (bp) fragment of the mitochondrial cytochrome c variants within species (Avise 1989; Moritz 1994, 2002; oxidase subunit one (COI) gene to identify and delin- Vogler and DeSalle 1994; Bowen 1998, 1999; Grady eate species (Hebert et al. 2003a, b). This approach has and Quattro 1999; Paetkau 1999; Crandall et al. 2000; some advantages, including the ability to obtain taxo- Goldstein et al. 2000; Fraser and Bernatchez 2001; nomic information from portions or fragments of Agapow et al. 2004). Increasingly, molecular taxonomy organisms, its applicability at any life stage (e.g. Sper- and phylogenetic analyses have been used to identify ling et al. 1994; Greenstone et al. 2005; Miller et al. ESUs, based upon the assumption that historically 2005), and the speed with which data can be obtained. distinct populations have the greatest potential to The concept of using DNA to identify an organism is contain distinct adaptive variation. However, earlier not new, and routinely employs a BLAST (Basic Local incarnations of the ESU included the use of other Alignment Search Tool) search on NCBI’s (National information in addition to molecular data: ‘‘Identifi- Center for Biotechnology) GenBank or similar data- cation of ESUs within a species was recognized as a bases (Tautz et al. 2003; Hebert et al. 2004b). DNA difficult task, requiring the use of natural history barcoding is simply an attempt to standardize which information, morphometrics, range and distribution piece of DNA is used. data, as well as protein electrophoresis, cytogenetic The arguments put forth by proponents of DNA analysis, and restriction mapping of nuclear and mito- barcoding strongly suggest that molecular approaches chondrial DNA’’ (Ryder 1986). For a population to be and a common database will be increasingly useful designated as an ESU based solely on sequence vari- for identification. In essence, the molecular database ation at a single marker locus ignores the fact that will act as a ‘‘molecular field guide,’’ facilitating adaptive evolution and population differentiation can identifications. They also argue that discovery of proceed at a rapid pace compared to rates of molecular cryptic species will be enhanced with this approach. evolution at a presumably neutral marker. Thus, his- Discovery of cryptic variation has long been the torical isolation would trump morphological, life his- purview of molecular phylogenetics and the utility of tory, and ecological discontinuities discordant with molecular approaches for this aspect of identification molecular data. Despite the claim that molecular is undeniable (Donnellan and Aplin 1989; Good phylogenetic approaches will provide a more accurate 1989). In fact, some molecular phylogeneticists have view of biodiversity (Hebert et al. 2003a, b; but see 123 J Insect Conserv (2008) 12:37–51 39 Brower 2006), a number of processes occurring at or or identify the taxa in question. Studies which simply below the species level, including recent differentiation surveyed genetic variation within ecologically or mor- and hybridization, will result in an underestimation of phologically polymorphic species without any particular biodiversity. expectation of reproductive isolation or genetic diver- Our principal objectives are to provide researchers gence among taxa were not considered. and conservation managers with a discussion of pat- The following key words generated 437 studies in terns and processes at or near the species level