1. Introduction
The distinctiveness of giant tortoises (Geochelone nigra) throughout the Galápagos archipelago was an inspiration to Charles Darwin in developing his theory of natural selection as the mechanism of biological evolution. Fifteen formally described taxa of G. nigra are generally recognized, 11 of which are extant and threatened by human activities and introductions of non-native species (Pritchard 1996). The prevailing taxonomy is largely based on morphological differences among populations, primarily in carapace (shell) shape, which varies from domed to saddleback with intermediate forms also occurring (Fritts 1984). The taxonomic rank of populations that are often morphologically distinct on different islands and volcanoes has been contentious, especially as to whether such populations should be considered different species or subspecies (here referred to simply as taxa or lineages; Zug 1997). Our previous molecular studies have confirmed the distinctiveness of the extant named taxa (Caccone et al. 2002; Ciofi et al. 2002; Beheregaray et al. 2003; Beheregaray et al. 2004).
Santa Cruz is a moderately sized island central to the archipelago (figure 1; White et al. 1993) that supports one of the largest remaining populations of tortoises (ca 2000-4000 individuals). Paradoxically, this island also maintains the largest human population in Galápagos (currently greater than 20000 and anticipated to double by 2013; MacFarland & Cifuentes 1995); thus, its unique biota is under heavy pressure from anthropogenic activities, including the conversion of substantial natural habitat for agriculture (figure 1). A single domed taxon of G. nigra has been described on Santa Cruz and given the name porteri (Fritts 1984). Two major populations of porteri occur on the island, each separated by urban and farm lands; one in the southwest Santa Rosa Tortoise Preserve ('La Caseta'; figure 1) and the other to the east of the city of Puerto Ayora ('Cerro Fatal'; figure 1). In addition, a very small, isolated population exhibiting the saddleback morphology has been documented in the northwest of Santa Cruz in an area called Cerro Montura (figure 1). While morphologically distinct from the domed porteri typical of Santa Cruz, it has never been assigned a formal Latinized name and is generally considered to be restricted to a few individuals in the wild, where only a single female and two males have been observed.
Previous studies (Caccone et al. 2002; Beheregaray et al. 2003) have hinted at a deep split among the extant lineages on Santa Cruz yet sampling limitations precluded a definitive evaluation of their genetic distinctiveness, taxonomic status and time of colonization. To explicitly address these questions, we conducted a comprehensive sampling of the Cerro Fatal and Cerro Montura populations on Santa Cruz to augment previous collections from La Caseta (Ciofi et al. 2002), and expanded character sampling by way of mitochondrial DNA (mtDNA) sequencing and microsatellite genotyping. Moreover, to specifically address the timing and origin of the Santa Cruz lineages, we have also included DNA sequence data from museum specimens of two extinct but biogeographically relevant taxa from the islands of Floreana and San Cristóbal (figure 1), the latter hypothesized as the source from which all other domed taxa may have been derived, including those currently extant on Santa Cruz.
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