Testing Species Boundaries in an Ancient Species Complex with Deep Phylogeographic History: GenusXantusia(Squamata: Xantusiidae)

Abstract

Identification of species in natural populations has recently received increased attention with a number of investigators proposing rigorous methods for species delimitation. Morphologically conservative species (or species complexes) with deep phylogenetic histories (and limited gene flow) are likely to pose particular problems when attempting to delimit species, yet this is crucial to comparative studies of the geography of speciation. We apply two methods of species delimitation to an ancient group of lizards (genus Xantusia) that occur throughout southwestern North America. Mitochondrial cytochrome b and nicotinamide adenine dinucleotide dehydrogenase subunit 4 gene sequences were generated from samples taken throughout the geographic range of Xantusia. Maximum likelihood, Bayesian, and nested cladogram analyses were used to estimate relationships among haplotypes and to infer evolutionary processes. We found multiple well-supported independent lineages within Xantusia, for which there is considerable discordance with the currently recognized taxonomy. High levels of sequence divergence (21.3%) suggest that the pattern in Xantusia may predate the vicariant events usually hypothesized for the fauna of the Baja California peninsula, and the existence of deeply divergent clades (18.8%-26.9%) elsewhere in the complex indicates the occurrence of ancient sundering events whose genetic signatures were not erased by the late Wisconsin vegetation changes. We present a revised taxonomic arrangement for this genus consistent with the distinct mtDNA lineages and discuss the phylogeographic history of this genus as a model system for studies of speciation in North American deserts.

Phylogeography of Supralittoral Rocky Intertidal Ligia Isopods in the Pacific Region from Central California to Central Mexico

“…Ligia , on the other hand, is unlikely to be affected by inland habitat changes as suggested by its wide distribution. Perhaps the only phylogeographic studies that do include samples from the southern mainland are on Xantusia lizards [51] and on Trimorphodon snakes [69]. As mentioned above, Xantusia shows a similar pattern to Ligia .…”

“…A ∼1 Ma mid-peninsular seaway was originally proposed to explain a mid-peninsular divergence of Uta lizards [28], but the same research group indicates in subsequent papers that this divergence may represent Late Miocene–Early Pliocene times [24], [49], [50]. Mid-peninsular phylogeographic breaks have been reported in multiple taxa [e.g., 22]; but a broad range of divergences is observed, with some showing deep [46], [49], [51], while others shallower phylogeographic breaks [22]. Riginos [52] suggests that a Plio-Pleistocene mid-peninsular seaway is the simplest explanation for a concordant genetic division within both terrestrial and marine vertebrates.…”

“…They have a circum-Gulf of California distribution; comprise a large number of allopatric populations with high levels of genetic divergence; and, have an extremely patchy distribution, limited vagility, and close association with particular structural niches [51]. As in Ligia , northern and southern Baja lineages of Xantusia cluster in two separate clades that are highly divergent (i.e., ∼22% for Cytb and ND4 mitochondrial genes); possibly representing a Miocene separation [51]. In addition, Xantusia lineages from southern Baja, including the Cape region, are more closely related to lineages in mainland localities that are found inland south of latitude 25°N (see Fig.…”

Phylogenetic Analysis of Ecomorphological Divergence, Community Structure, and Diversification Rates in Dusky Salamanders (Plethodontidae: Desmognathus)

“…Well-supported groupings of haplotype clades that are concordant with geography delimit independent populational lineages concealed by previous taxonomy. Inclusion of as many species as possible that are closely related to the focal species is crucial, because a focal species may be nonexclusive for haplotypic variation and may comprise multiple cryptic lineages that are not each other's closest relatives (e.g., Sinclair et al 2004).…”

Historical Environment Is Reflected in Modern Population Genetics and Biogeography of an Island Endemic Lizard (Xantusia riversiana reticulata)

“…Xantusia riversiana may be the sister species to all other members of the genus, from which it diverged approximately 14 to 16 MYA ([23]; but see [30] and [31] for alternative tree topologies and divergence time estimates). At that time, the flora of Baja California was primarily tropical deciduous forest, with evergreen broadleaf forest present in riparian areas [32].…”