Interphotoreceptor Retinoid-binding Protein Gene Research Articles

Molecular assessment of the taxonomic status of pine vole species Microtus subterraneus and Microtus majori in southeastern Europe and Turkey

Intra– and inter–specific phylogenetic relationships and the taxonomic status of pine vole populations have been controversial for years, and cryptic species are thought to exist, especially concering the species' distribution area. To clarify the taxonomic status of Turkish populations we analysed mitochondrial (cytochrome–b and cytochrome oxidase–I) and nuclear (interphotoreceptor retinoid binding protein) gene markers, adding GenBank data from Europe and Caucasia. Considering the data obtained based on mean genetic distance, genetic diversity and fixation index values, Bayesian trees and Median–joining networks, we found that M. subterraneus and M. majori are valid species which have diverged since 1.28 Mya. Findings also suggested that although Anatolian, Thracian (Turkish Thrace and Greece) and European populations of M. subterraneus and Anatolian and Caucasian populations of M. majori have been in the process of divergency since 0.528–0.337 Mya correspond to the Pleistocene glacial periods, these intrapopulations do not appear to be different species.Besides, considering the high intraspecific variation in M. subterraneus, it remains likely that new species could be identified in future studies.

Comparative genetic research on Microtus mystacinus (de Filippi, 1865) distributed in Asia and Europe inferred from mitochondrial (CYTB and COXI) and nuclear (IRBP) gene regions

Abstract The East European vole Microtus mystacinus is the most widespread vole species in Anatolia. It is also frequently seen in watery habitats in a large area of Eurasia. In this paper, an attempt was made to ascertain the level of genetic differentiation between Anatolian (Asian part of Turkey) and Turkish Thracian (European part of Turkey) populations together with additional data from other parts of Asia and Europe by analysing two mitochondrial (cytochrome-b and cytochrome oxidase subunit I) and one nuclear (interphotoreceptor retinoid binding protein) gene regions. Acquired Bayesian Inference trees mostly separated the Asian and European populations of M. mystacinus and the fixation index values implied a significant differentiation between these populations for mitochondrial DNA. On the other hand, the median-joining networks did not show diverging populations, significantly, and the mean genetic distance values among populations were found to be low for both mitochondrial and nuclear DNA. Evolutionary divergence times of Asian and European populations were also calculated and dated back to approximately 0.316–0.111 million years ago, coinciding with the ice ages of the Pleistocene epoch. According to the obtained results, M. mystacinus populations have not diverged enough to form different species; however, there is a separation between Asian and European populations which might result in speciation.

Molecular characterization and phylogeography of Mediterranean picarels (Spicara flexuosa, S. maena and S. smaris) along the coasts of Turkey and the Eastern Mediterranean

In this study, molecular taxonomy associated with Spicara flexuosa, Spicara maena, and Spicara smaris was examined with a geographical focus along the coasts of the Turkey and the Mediterranean. In addition, the effects of the Turkish Straits System on the evolutionary history and phylogeography of Spicara flexuosa were investigated. The mitochondrial cytochrome c oxidase I, cytochrome b, and the nuclear Interphotoreceptor retinoid–binding protein genes were used for these purposes. Our results indicated that the distinction of the three taxa under Spicara is possible with the two different mitochondrial DNA markers. Nuclear DNA analyses indicated that reproductive isolation of the S. maena and S. flexuosa was complete. Demographic analyses support the sudden population growth of S. flexuosa after a potential bottleneck. The result of the dating analyses suggested that the three Spicara species were differentiated during the early or middle Pliocene. An absence of genetic structure between Spicara flexuosa subpopulations from Turkey indicated the connectivity, within sampling locations, suggesting that the Turkish Straits System is a corridor for gene flow for this species. As picarel populations have experienced rapid decline in their distribution areas in recent years, separate population studies are necessary to help make informed conservation and management decisions for S. maena and S. flexuosa.

The roles of possible geographic barriers and geological events on the phylogeographic structure of the Eastern broad toothed field mouse (Apodemus mystacinus)

Abstract The Eastern broad toothed field mouse, Apodemus mystacinus, is a rodent species distributed in Turkey, the Middle East, and a few Aegean Islands. The aim of this study is to analyse the phylogeographic structure of A. mystacinus and possible causes of its differentiation, on the basis of mitochondrial and nuclear DNA sequences using a large number of new samples from Turkey. In this context, partial mitochondrial sequences of cytochrome b (Cytb), control region (D-loop) and a nuclear interphotoreceptor retinoid-binding protein (IRBP) gene were used to reveal the geographical differentiation among A. mystacinus populations and the validity of its subspecies. The estimated divergence times revealed that the first separation of A. mystacinus into three distinct groups (subspecies of A. mystacinus: A. m. mystacinus, A. m. smyrnensis, and A. m. euxinus) begun 0.641 Mya. The possible physical barriers in Anatolia such as high mountains and rivers could interrupt the gene flow between A. mystacinus populations. The results of the present study indicated that A. mystacinus might have used the high rocky areas along the Anatolian Diagonal as a dispersal way. Moreover, mitochondrial data in this study suggested for the first time that A. m. rhodius is synonymous with the nominative subspecies A. m. mystacinus.

Detection and identification of Kinetoplastids of zoonotic interest by HRM-qPCR analysis in Canis lupus familiaris from Argentinean Mesopotamia.

This work aimed to conduct a first PCR-based approach for differential diagnosis of kinetoplastidean infections in dogs. Diagnosis of Kinetoplastid infections in domestic animals is difficult, since parasitemia is intermittent and signs are nonspecific; it is mainly based on parasitological smears or concentration techniques, which lack sensitivity and depend on operator` expertise. Dogs are relevant reservoirs in transmission of Kinetoplastids; they function as sentinels to detect active transmission cycles before they involve humans. Trypanosoma cruzi, Trypanosoma evansi, and various species of Leishmania genus are multi-host parasites, capable of parasitizing dogs among a vast number of reservoirs. An algorithm based on sequential Real-Time PCR-High Resolution Melting (HRM) (qPCR-HRM) assays directed at 24S alpha ribosomal DNA, ITS1 and Hsp70 designed to distinguish among T. cruzi, T. rangeli, T. evansi and Leishmania spp. was tested in fourteen dogs with suspicion of kinetoplastid diseases. A qPCR control of DNA integrity in the tested sample, targeted to the mammalian interphotoreceptor retinoid-binding protein (IRBP) gene fragment was incorporated to the algorithm. T. evansi was detected in four dogs and L. infantum in one. Two of five qPCR positive cases were smear negative. Smear and T. evansi qPCR positive cases corresponded to animals that died despite being treated, indicating the association of parasitemia with disease severity. This laboratory tool increases the possibility of confirming outbreaks of kinetoplastid diseases with zoonotic potential and identify the etiological agents involved.

First detection of Leishmania of the subgenus viannia in Alipiopsitta xanthops, endemic bird of South America

We report the first molecular detection of Leishmania infection (subgenus Viannia) in the yellow-faced parrot (Alipiopsitta xanthops), at a wildlife rehabilitation center located in the city of Campo Grande, Brazil, an endemic area for leishmaniasis. PCRs targeting kinetoplast DNA (kDNA) and the small subunit of ribosomal RNA of Leishmania spp. were performed, both positive, followed by the sequencing of the amplified region of the SSU rDNA gene, which confirmed the identity of the parasite. This is the first report of success obtained in the use of PCR targeting the IRBP (Interphotoreceptor retinoid-binding protein) gene as an internal control in the molecular diagnosis of pathogens in bird species.

Phylogenetic and morphological significance of an overlooked flying squirrel (Pteromyini, Rodentia) from the eastern Himalayas with the description of a new genus.

The flying squirrels (Pteromyini, Rodentia) are the most diverse and widely distributed group of gliding mammals. Taxonomic boundaries and relationships within flying squirrels remain an area of active research in mammalogy. The discovery of new specimens of Pteromys (Hylopetes) leonardi Thomas, 1921, previously considered a synonym of Hylopetes alboniger, in Yunnan Province, China allowed a morphological and genetic reassessment of the status of this taxon. Phylogenetic reconstruction was implemented using sequences of two mitochondrial (12S ribosomal RNA and 16S ribosomal RNA) and one nuclear (interphotoreceptor retinoid-binding protein) gene fragments. Morphological assessments involved examinations of features preserved on skins, skulls, and penises of museum specimens, supplemented with principal component analysis of craniometric data. Together these assessments revealed that this taxon should be recognized not only as a distinct species, but should also be placed within a new genus, described here as Priapomysgen. nov.

Taxonomy and Phylogeny of Sibling-Species Sicista of the Group Caucasica and Their Position in the Genus Sicista (Rodentia, Dipodoidea) according to Sequencing of the IRBP Gene Fragment of Nuclear DNA

To specificate phylogenetic relationships between sibling-species Sicista of the caucasica group and to determine their position in the genus Sicista, comparative analysis of the nucleotide sequences of a fragment (903 bp) of the first exon of the IRBP (interphotoreceptor retinoid-binding protein) gene of nuclear DNA has been carried out for three Sicista species (S. caucasica, S. kluchorica, and S. kazbegica) of the caucasica group. Some other Sicista species (S. concolor, S. tianschanica, and Sicista species of the groups betulina and subtilis) have been taken for comparison. The results reflect the monophyly of the group and its division into the three clades corresponding to sibling-species of the group. It has been shown that the average genetic distances between S. caucasica and S. kluchorica calculated on the nucleotide sequences of a fragment (903 bp) of the first exon of IRBP gene using three-parametrical Tamura’s model (T92) do not exceed 0.4%. The level of differences of each of these two species from S. kazbegica is 0.7%, which is comparable to the interspecific genetic distances for Sicista sibling-species of the group betulina (intergroup genetic distances exceed 2%).

Genetic legacy of tertiary climatic change: a case study of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi, in Hong Kong.

The high biodiversity and strong population structure of freshwater fauna has often been attributed to historical geological and climatic alterations. The impact of these historical changes on obligate freshwater species on a small geographical scale has not been well understood due to the lack of fine-scale comparative phylogeographic studies. Strong population structure has been reported in a goby and a caridean shrimp in Hong Kong, a small but highly developed city in South China, but the common drivers of population differentiation in freshwater fauna in this region remain unclear. This study examined the fine-scale phylogeographic patterns of two freshwater loaches, Schistura fasciolata and Pseudogastromyzon myersi in Hong Kong, using sequence data of mitochondrial control region and two nuclear markers (interphotoreceptor retinoid binding protein gene 2 and ribosomal protein S13 gene). Results show that they exhibit pronounced population structure as supported by high and significant ΦST. Phylogenetic analyses based on the control region reveal six and three distinct lineages in S. fasciolata and P. myersi, respectively. Phylogeographic structure of both species generally follows the paleodrainage pattern, though P. myersi shows a shallower structure on the Mainland, perhaps due to their higher mobility. Most of these lineages diverged during the Pliocene and Late Pleistocene, a period with marked sea-level fluctuations. In a broader context, this suggests that sea-level fluctuation played an important role in shaping even the fine-scale population structure of freshwater fish in South China, implying that the genetic diversity of this fauna may be higher than expected.

Molecular systematics of the Labeonini inhabiting the karst regions in southwest China (Teleostei, Cypriniformes).

The major phylogenetic pattern of the cyprinid tribe Labeonini has been revealed by previous molecular studies; however, the relationships within a clade that mainly inhabits the karst regions, which we refer to as the “karst group”, in southwest China remain unresolved due to the low taxon sampling. This group includes more than 50% of the genera and species of Labeonini in China. Moreover, more than 90% of the genera of this group are endemic to China. In addition, some new genera and species of Labeonini have been discovered from these karst regions, but their taxonomic validity and phylogenetic position have not been examined. In this contribution, partial sequences of four nuclear (exon 3 of recombination activating protein 1, rhodopsin, early growth response protein 2B gene and interphotoreceptor retinoid binding protein gene) and three mitochondrial genes (cytochrome b, cytochrome oxidase subunit I and 16S ribosomal RNA) from 36 ingroup taxa and 25 outgroup taxa were analyzed to provide a hypothesis of the phylogenetic relationships within the labeonins of the karst regions in China. We propose that the monophyly of Parasinilabeo, Ptychidio, Rectoris and Semilabeo are supported. A new genus, Prolixicheilus, is erected for Pseudogyrinocheilus longisulcus. Cophecheilus bamen is the sister to Prolixicheilus longisulcus. Ptychidio, Pseudocrossocheilus, Semilabeo, Rectoris and Stenorynchoacrum are closely related with high support values. Sinocrossocheilus, Pseudogyrinocheilus, Paraqianlabeo, Hongshuia, Discogobio and Discocheilus form a clade together with high support. Considering molecular results and morphological differences, Parasinilabeo longicorpus and Ptychidio macrops might be the synonyms of Parasinilabeo assimilis and Ptychidio jordani respectively. Comprehensive taxonomic revisions of the two genera Parasinilabeo and Ptychidio may be necessary.

A new species of fish-eating rat, genus Neusticomys (Sigmodontinae), from Ecuador.

Inthis study, the genetic substructure and morphology of the species Neusticomysmonticolus was evaluated. A nuclear marker and mitochondrial maker were used to examine phylogeographic structure and to estimategenetic distances. Two statistical measurement analyses were applied to morphological data. These data recovered two morphologically distinct phylogeographic groups corresponding to populations on the eastern and western slopes of the Andes. Further, these eastern and western Andean slope populations of N. monticolus are 8.5 % divergent using sequence data from cytochrome-b (0.8 % divergent in the interphotoreceptor retinoid-binding protein gene). Populationscurrently assigned to N.monticolus constitutea species complex. The name N.monticolus is here restricted to western Andean slope populations. Populations on the eastern slope of the Andes are assigned to a new species, to which the authors assign the name Neusticomys vossi sp.nov.

An enigmatic pygmy dormouse: molecular and morphological evidence for the species taxonomic status of Typhlomys chapensis (Rodentia: Platacanthomyidae)

The taxonomic position of enigmatic pygmy dormouse Typhlomys (Rodentia: Platacanthomyidae) from Vietnam is reconsidered based on both morphology and sequence data. The analysis of mitochondrial and nuclear genes has shown that the pygmy dormouse from Lao Cai Province of northern Vietnam belongs to a distinct phylogenetic lineage of Typhlomys. The DNA analysis has demonstrated a strong genetic difference (0.245 to 0.252 for the cytochrome oxidase gene (COI), 0.079 to 0.082 for interphotoreceptor retinoid-binding protein gene (IRBP), and 0.028 for the growth hormone receptor gene (GHR) between this lineage and the sample from South China. Multivariate analysis of cranial and dental data, as well as of some external characters, has also separated the Vietnamese population from the pygmy dormouse from Fujian in southern China, the type locality of Typhlomys cinereus (Bull Soc Philomath Paris 12:8–10, 1877). Both genetic and morphological data confirm that there is a second species, Typhlomys chapensis (Field Mus Nat Hist Zool Ser 18:193–339, 1932), in the heretofore monotypic genus Typhlomys.

Cryptic divergence and revised species taxonomy within the Great Basin pocket mouse,Perognathus parvus(Peale, 1848), species group

The Great Basin pocket mouse, Perognathus parvus, inhabits temperate shrub-steppe and arid grassland biomes throughout the Columbia Plateau, Great Basin, and adjacent regions of western North America. We used both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) sequences to address phylogenetic and biogeographic structure within the P. parvus species group. Phylogenetic and biogeographic analyses divide haplotypes from the mtDNA cytochrome oxidase subunit 3 (COIII) gene into largely allopatric northern versus southern lineages (clades), with divergences of up to 18.8%. The southern mtDNA clade also includes at least 1 of the 2 recently extant populations of the white-eared pocket mouse, P. alticolus—an endangered species with a restricted range in southern California. The northern mtDNA clade is further subdivided into several additional lineages with divergences as high as 8.8%, whereas the southern clade has no divergence greater than 1.2%. The deeper mtDNA gene tree structure was recovered by use of nDNA exon sequences from the interphotoreceptor retinoid-binding protein (IRBP) and recombination activating gene 2 (RAG2) gene regions, supporting a “gene tree–species tree” congruence. We estimated through molecular clock analyses that the northern and southern clades likely diverged within a late Miocene time frame. The limited available karyological evidence is consistent with a genome-wide divergence between northern and southern clades—thus, is consistent with recognition of each as a separate species. Conversely, our morphometric analysis revealed a high level of morphological conservatism without detectable diagnostic differences, rendering them as “cryptic” species. We revised species-level taxonomy, designating 2 neotypes given apparent loss of original type specimens. We postulate that barriers associated with Columbia Plateau, Snake River Plain, and Great Basin physiographic evolution, during a Neogene time frame, resulted in persistent geographic isolation driving divergence between the northern and southern clades.

Cytonuclear discordance among Southeast Asian black rats (Rattus rattus complex)

Black rats are major invasive vertebrate pests with severe ecological, economic and health impacts. Remarkably, their evolutionary history has received little attention, and there is no firm agreement on how many species should be recognized within the black rat complex. This species complex is native to India and Southeast Asia. According to current taxonomic classification, there are three taxa living in sympatry in several parts of Thailand, Cambodia and Lao People's Democratic Republic, where this study was conducted: two accepted species (Rattus tanezumi, Rattus sakeratensis) and an additional mitochondrial lineage of unclear taxonomic status referred to here as 'Rattus R3'. We used extensive sampling, morphological data and diverse genetic markers differing in rates of evolution and parental inheritance (two mitochondrial DNA genes, one nuclear gene and eight microsatellite loci) to assess the reproductive isolation of these three taxa. Two close Asian relatives, Rattus argentiventer and Rattus exulans, were also included in the genetic analyses. Genetic analyses revealed discordance between the mitochondrial and nuclear data. Mitochondrial phylogeny studies identified three reciprocally monophyletic clades in the black rat complex. However, studies of the phylogeny of the nuclear exon interphotoreceptor retinoid-binding protein gene and clustering and assignation analyses with eight microsatellites failed to separate R.tanezumi and R3. Morphometric analyses were consistent with nuclear data. The incongruence between mitochondrial and nuclear (and morphological) data rendered R.tanezumi/R3 paraphyletic for mitochondrial lineages with respect to R.sakeratensis. Various evolutionary processes, such as shared ancestral polymorphism and incomplete lineage sorting or hybridization with massive mitochondrial introgression between species, may account for this unusual genetic pattern in mammals.

Phylogenetics and biogeography of the microendemic rodentXerospermophilus perotensis(Perote ground squirrel) in the Oriental Basin of Mexico

Phylogenetic relationships of the Mexican endemic and endangered Perote ground squirrel, Xerospermophilus perotensis (Rodentia: Sciuridae), were examined using 2 mitochondrial (cytochrome-b [Cytb] and 12S ribosomal RNA) and 2 nuclear (growth hormone receptor and interphotoreceptor retinoid-binding protein) genes for a total of 3,403 base pairs. Gene sequences were analyzed using maximum-likelihood and Bayesian models of phylogenetic inference. Independent analyses of the 4 gene sequences converged on essentially identical gene

A newly recognized clade of trans-Andean Oryzomyini (Rodentia: Cricetidae), with description of a new genus

Abstract We expand upon recent studies on relationships within the Oryzomyini, in particular, those involving taxa currently assigned to the genus Sigmodontomys. In recent years, Sigmodontomys has been treated as including 2 species, alfari (J. A. Allen, 1897) and aphrastus (Harris, 1932), but throughout their complicated taxonomic history both species also have been placed in the genus Oryzomys, and alfari independently in Nectomys. Using morphological (98 external, cranial, dental, and postcranial) and molecular (nuclear interphotoreceptor retinoid–binding protein gene and mitochondrial cytochrome-b and ribosomal 12S RNA genes) characters, we infer the phylogenetic position of these 2 species within Oryzomyini. We document that alfari and aphrastus do not form a monophyletic group. Sigmodontomys alfari is most closely related to Melanomys, and aphrastus is either the sister to that clade, or to the extinct Caribbean genus Megalomys. Thus, aphrastus is best regarded as representing a new genus, which is ...

Molecular systematics and biogeography of the Mexican endemic kangaroo rat,Dipodomys phillipsii(Rodentia: Heteromyidae)

We examined the phylogenetic relationships among populations of the Mexican endemic and endangered Phillips’ kangaroo rat, Dipodomys phillipsii (Rodentia: Heteromyidae), using mitochondrial (cytochrome-b and 12S ribosomal RNA) and nuclear (growth hormone receptor and interphotoreceptor retinoid-binding protein) genes for a total of 3,110 base pairs. Gene sequences were analyzed under maximum-likelihood and Bayesian models of phylogenetic inference. Analyses of the mitochondrial genes converged on essentially identical gene trees in which D. phillipsii is divided into 2 well-supported clades. The Mexican Plateau clade of D. phillipsii, formerly recognized as D. p. ornatus, is herein returned to full species status as D. ornatus. The southern clade of D. phillipsii retains the subspecies D. p. oaxacae, D. p. perotensis, and D. p. phillipsii. D. ornatus, D. phillipsii, D. elator, and D. merriami form a well-supported, but unresolved polytomy. Analyses of the nuclear genes show the same fundamental subdivision within D. phillipsii but do not provide additional resolution within the 4-species polytomy. Based on analyses of divergence times, we place the separation of these 4 species near the middle Pliocene, which suggests that the morphotectonic processes that gave rise to the TransMexico Volcanic Belt may have influenced diversification in Mexican species of Dipodomys. Synonymies of D. phillipsii and D. ornatus are provided along with a key to the subspecies of D. phillipsi and D. ornatus.

Phylogenetic relationships and phylogeographic patterns inMonodelphis(Didelphimorphia: Didelphidae)

Monodelphis (short-tailed opossums) is the most speciose South American marsupial genus, wtih species distributed from Panama to Argentina. The goal of the present study was to analyze levels and patterns of genetic variation in M. brevicaudata (Guianan short-tailed opossum), M. dimidiata (yellow-sided opossum), M. domestica (gray short-tailed opossum), and M. kunsi (pygmy short-tailed opossum) using sequences of the mitochondrial cytochrome b (Cytb) and nuclear interphotoreceptor retinoid-binding protein (IRBP) genes from individuals sampled in the Amazon, Cerrado, Caatinga, Atlantic Forest, and Pampa biomes in Brazil. Species relationships also were analyzed using sequences of 9 other Monodelphis species retrieved from GenBank and representing 3 localities in Brazil and 17 sites in other South American countries. M. domestica and M. brevicaudata showed phylogeographic structure, but M. dimidiata and M. kunsi did not. Maximum parsimony, maximum likelihood, and Bayesian algorithms showed similar topologies for estimated phylogenetic trees. Analyses of individual genes produced comparable results, but combined loci produced trees with higher support. All Monodelphis haplotypes were monophyletic, with M. emiliae (Emilia's short-tailed opossum) sister to all other species, which form 2 groups. M. brevicaudata (from the Amazon) forms a well-supported clade with M. domestica (which occupies several biomes) and 2 unidentified Amazonian species. The other branch has M. kunsi (from the Cerrado) as sister to a well-supported clade of 5 Amazonian species.

Alternative PCR protocol using a single primer set for assessing DNA quality in several tissues from a large variety of mammalian species living in areas endemic for leishmaniasis

The aim of this work was to establish a modified pre-diagnostic polymerase chain reaction (PCR) protocol using a single primer set that enables successful amplification of a highly conserved mammalian sequence in order to determine overall sample DNA quality for multiple mammalian species that inhabit areas endemic for leishmaniasis. The gene encoding interphotoreceptor retinoid-binding protein (IRBP), but not other conserved genes, was efficiently amplified in DNA samples from tail skin, ear skin, bone marrow, liver and spleen from all of the species tested. In tissue samples that were PCR-positive for Leishmania, we found that DNA from 100%, 55% and 22% of the samples tested resulted in a positive PCR reaction for the IRBP, beta-actin and beta-globin genes, respectively. Nucleotide sequencing of an IRBP amplicon resolved any questions regarding the taxonomical classification of a rodent, which was previously based simply on the morphological features of the animal. Therefore, PCR amplification and analysis of the IRBP amplicon are suitable for pre-diagnostically assessing DNA quality and identifying mammalian species living in areas endemic to leishmaniasis and other diseases.

Diversification of the Perognathus flavus species group in emerging arid grasslands of western North America

We investigated the evolutionary history of a group of silky pocket mice (Heteromyidae: Perognathinae: Perognathus flavus species group) composed of the species P. flavus and P. merriami to determine patterns and postulate causes of geographical diversification across arid grasslands and intermontane basins in western North America. The region represents a topographically complex landscape with a Neogene history of dramatic geological and climatic transformations. Phylogenetic and dating analyses of mitochondrial DNA support an initial split among 4 major lineages during the late Miocene, and this hypothesis receives further support from analysis of a portion of the nuclear interphotoreceptor retinoid-binding protein (IRBP) gene. Two of these lineages have a restricted geographic distribution in the Chihuahuan Desert, and 2 have distributions ranging across large portions of the Chihuahuan Desert, Colorado Plateau, Great Plains, and Tamaulipan Plain. Within the 2 widespread lineages further geographical diversification likely was concentrated in the Pliocene, which coincided with the origin of several hypothesized geographic barriers. These results are consistent with models of allopatric divergence driven by pre-Pleistocene geological and climatic events, particularly the late-Miocene expansion of interior grasslands and Miocene–Pliocene evolution of Basin and Range geomorphology. Therefore, the biogeographic structure displayed in the flavus species group may be predictive for a range of sympatric taxa. DOI: 10.1644/09-MAMM-A-102.1.