Ridges and rivers: a test of competing hypotheses of Amazonian diversification using a dart-poison frog (Epipedobates femoralis).

Mitochondrial DNA cytochrome b sequence data from a dart-poison frog, Epipedobates femoralis, were used to test two hypotheses of Amazonian diversification: the riverine barrier and the ridge hypotheses. Samples were derived from sites located on both banks of the Rio Juruá and on both sides of the Iquitos Arch in western Amazonia. The phylogeographic structure was inconsistent with predictions of the riverine barrier hypothesis. Haplotypes from opposite river banks did not form monophyletic clades in any of our phylogenetic analyses, nor was the topology within major clades consistent with the riverine hypothesis. Further, the greatest differentiation between paired sites on opposite banks was not at the river mouth where the strongest barrier to gene flow was predicted to occur. The results instead were consistent with the hypothesis that ancient ridges (arches), no longer evident on the landscape, have shaped the phylogeographic relationships of Amazonian taxa. Two robustly supported clades map onto opposite sides of the Iquitos Arch. The mean haplotypic divergence between the two clades, in excess of 12%, suggests that this cladogenic event dates to between five and 15 million years ago. These estimates span a period of major orogenesis in western South America and presumably the formation of these ancient ridges.     

Hierarchical genetic structure and gene flow in three sympatric species of Amazonian rodents

The population genetic structure of three species of Amazonian rodents ( Oligoryzomys microtis, Oryzomys capito , and Mesomys hispidus ) is examined for mtDNA sequence haplotypes of the cytochrome b gene by hierarchical analysis of variance and gene flow estimates based on fixation indices ( N _ST) and coalescence methods. Species samples are from the same localities along 1000 km of the Rio Juruá in western Amazonian Brazil, but each species differs in important life history traits such as population size and reproductive rate. Average haplotype differentiation, hierarchical haplotype apportionment, and gene flow estimates are contrasted in discussing the current and past population structure. Two species exhibit isolation by distance patterns wherein gene flow is largely limited to geographically adjacent localities. Mesomys exhibits this pattern throughout its range along the river. More than 75% of haplotype variation is apportioned among localities and regions, and estimates of Nm for pair-wise comparisons are nearly always less than 1. Oligoryzomys shows weak isolation by distance, but only over the largest geographical distances. Nm values for this species are nearly always above 1 and most (about 80%) of haplotype variation is contained within local populations. In contrast, Oryzomys exhibits no genetic structure throughout its entire distribution; Nm values average 17 and nearly 90% of the total haplotype variance is contained within local populations. Although gene flow estimates are high, the pattern of Nm as a function of geographical distance suggests that this species experienced a more recent invasion of the region and is still in genetic disequilibrium under its current demographic conditions.     

Hisonotus devidei,a new species from the São Francisco basin,Brazil (Siluriformes: Loricariidae)

A recent expedition to headwaters of the Rio Pandeiros, a left‐bank tributary of the Rio São Francisco revealed the presence of a fourth species of Hisonotus from that basin. Hisonotus devidei sp. nov. differs from congeners by the presence of conspicuous dark blotches of distinct shapes irregularly arranged along lateral and dorsal surfaces of the body and scattered throughout all fins, by possessing small plates in lateral portions of the abdomen and adjacent areas between pelvic fins without development of dermal plates and by morphometric ratios. The putative phylogenetic placement of the new species is discussed based on morphological comparisons with species of related Hypoptopomatinae genera and the Hisonotus species diversity within the Rio São Francisco Basin is compared with that of adjacent basins.     

Molecular systematics, biogeography and population structure of neotropical freshwater needlefishes of the genus Potamorrhaphis

Phylogenetic relationships of populations and species within Potamorrhaphis, a genus of freshwater South American needlefishes, were assessed using mitochondrial cytochrome b sequences. Samples were obtained from eight widely distributed localities in the Amazon and Orinoco rivers, and represented all three currently recognized species of Potamorrhaphis. The phylogeny of haplotypes corresponded imperfectly to current morphological species identities: haplotypes from P. guianensis, the most widespread species, did not make up a monophyletic clade. Geography played a strong role in structuring genetic variation: no haplotypes were shared between any localities, indicating restricted gene flow. Possible causes of this pattern include limited dispersal and the effects of current and past geographical barriers. The haplotype phylogeny also showed a complex relationship between fishes from different river basins. Based on the geographical distribution of clades, we hypothesize a connection between the middle Orinoco and Amazon via rivers of the Guianas. More ancient divergence events may have resulted from Miocene alterations of river drainage patterns. We also present limited data for two other Neotropical freshwater needlefish genera: Belonion and Pseudotylosurus. Pseudotylosurus showed evidence of substantial gene flow between distant localities, indicating ecological differences from Potamorrhaphis.     

Taxonomic revision of Hypostomus albopunctatus (Siluriformes: Loricariidae) reveals a new piece of the Hypostomus jigsaw in the upper Rio Paraná basin

Hypostomus albopunctatus was described from the Rio Piracicaba, a tributary of the Rio Tietê, upper Rio Paraná basin. Nevertheless, specimens attributed to this species are commonly found throughout other river systems in the upper Rio Paraná basin and present varying degrees of morphological variation. A taxonomic review of H. albopunctatus based on large series of specimens from many localities throughout the upper Rio Paraná basin was carried out. Results support H. lexi, H. niger and H. scaphyceps as junior synonyms. Hypostomus albopunctatus differs from all congeners except H. heraldoi by having pectoral-fin spine equal to or shorter than pelvic-fin spine (v. longer); it differs from H. heraldoi by having white or light yellow spots on the body and fins (v. dark brown or black spots). Despite conspicuous variation related to the shape and size of the spots and snout morphology, both spot and snout patterns overlapped among the examined populations, thus this variation was inferred to be intraspecific within a widely distributed H. albopunctatus.     

Moenkhausia celibela: a new species from the Amazon basin,Brazil (Characiformes: Characidae)

A new species of Characidae, Moenkhausia celibela, is described from the Rio Amazonas at Santarém, Rio Maraú, several localities in the Rio Tapajós, Rio Curuá‐Una, Rio Xingu and Rio Jari, all from the Amazon basin, Brazil. The new species is distinguished from its congeners, except species included in Géry's 1992 Moenkhausia lepidura group, by presenting a dark blotch on the upper caudal‐fin lobe, and the lower lobe is hyaline or light grey. Moenkhausia celibela is distinguished from the species of the M. lepidura group by the absence of a humeral spot and the presence of a roughly triangular and dark spot at the caudal‐fin base, extending posteriorly along the middle caudal‐fin rays, and distinctly separate from the spot on the upper caudal‐fin lobe.     

Exploring factors shaping population genetic structure of the freshwater fish Sinocyclocheilus grahami (Teleostei, Cyprinidae)

Phylogeographical analyses on Sinocyclocheilus grahami samples from seven localities within the Lake Dianchi Basin in China were conducted to explore the main factors shaping population structure within this species. Phylogenetic and network analyses revealed two major clades in 24 mtDNA haplotypes. One clade included three haplotypes exclusively from samples of the lower basin and another clade encompassed other haplotypes from samples of the upper basin. The estimated divergence time between the two clades predated the river capture event connecting the lower and upper lake basin and thus supported geographical isolation as the main factor shaping genetic divergence between these two clades. Furthermore, analysis of molecular variance and pair-wise Φ_ST distances revealed significant genetic differentiation within the upper basin. Mantel tests clearly supported patterns of differentiation arose purely as a result of isolation by distance. These results further highlight the importance of geographical isolation in shaping differentiation within this species.     

The Electric Glass Knifefishes of the Eigenmannia trilineata species‐group (Gymnotiformes: Sternopygidae): monophyly and description of seven new species

Eigenmannia trilineata López and Castello, 1966 (Sternopygidae) was described from the Río de La Plata basin and subsequently cited from most South American river basins. Questions about the limits of this species raise the possibility of the occurrence of undescribed species misidentified as E. trilineata. Herein we propose the Eigenmannia trilineata species group for species that share the presence of the superior medial stripe on the flank. This group comprises: E igenmannia antonioi sp. nov. , from the Rio Anapu, Rio Amazonas basin; E igenmannia desantanai sp. nov. , from the Rio Cuiabá, Rio Paraguay basin; E igenmannia guairaca sp. nov. , from the Riacho Água do Ó, upper Rio Paraná basin; E igenmannia matintapereira sp. nov. , from the Rio Uneiuxi and Rio Urubaxi, Rio Negro basin; Eigenmannia microstoma (Reinhardt, 1852), from the Rio São Francisco basin; E igenmannia muirapinima sp. nov. , from small tributaries of the Rio Amazonas; E igenmannia pavulagem sp. nov. , from the tributaries of Rio Capim, Rio Guamá basin; E. trilineata, from the lower Rio Paraná basin and Río de La Plata basin; Eigenmannia vicentespelaea Triques, 1996, from São Vicente I and II caves, Rio Tocantins basin; and E igenmannia waiwai sp. nov. , from the Rio Trombetas basin. These species can be distinguished from each other by unique sets of meristics, morphometrics, osteological and colour pattern features. © 2015 The Linnean Society of London     

Patterns of genetic diversity in the critically endangered Central American river turtle: human influence since the Mayan age?

We conducted a phylogeographic analysis of the strictly aquatic and critically endangered Central American river turtle, Dermatemys mawii, as part of a conservation management program for the species. We sampled 238 individuals from 15 different localities throughout the species range. Using sequence fragments from the mtDNA Cyt b and ND4 genes, we identified 16 different haplotypes. Overall, our results reveal a signal of phylogeographic structure throughout the range, which appears to have been secondarily blurred by extensive gene flow. Notably, this also applies to genetic structuring across three major hydrological basins that pose biogeographic breaks in other aquatic taxa. Divergence times of mtDNA haplotypes in D. mawii suggest that the main lineages split in the Pliocene–Pleistocene (3.73–0.227 MA) and demographic tests indicate that the species has undergone drastic demographic size fluctuations since this time period. One ancient haplotype (1D) was found to exhibit sequence divergence of up to 2% from other haplogroups. Divergence of this magnitude is indicative of species level differentiation in other turtle genera. Haplotype 1D was found in only two localities, Sarstun and Salinas, but specimens with other haplotypes were also found in those localities. It is not known whether the individuals with the 1D haplotype interbreed with non-1D individuals. Our results suggest that human activity, such as harvesting and long distance transport of animals, may have influenced the current patterns of genetic diversity. For more than 2000 years, D. mawii has been consumed by people from Middle American cultures, and the archeological record contains strong evidence that the Mayans transported animals between villages and far away from their natural distribution range. Therefore, the large-scale pattern of haplotype sharing even across hydrological barriers, the observed low haplotype diversity in some populations and the contemporary absence of a pronounced phylogeographic pattern is likely due to a combination of population expansions, gene flow, extensive human-mediated-movements and recent bottlenecks resulting from over-harvesting.     

Metazoan parasites as biological tags for stock discrimination of whitemouth croaker Micropogonias furnieri

Examination of 248 adult specimens of whitemouth croaker Micropogonias furnieri from five localities along the Brazilian coast revealed 8735 parasites belonging to 41 metazoan species. Samples from Ceará to Bahia and Rio de Janeiro to Santa Catarina showed a high level of correct assignation (92 and 87%, respectively) and cross assignation (i.e. almost all specimens misidentified in Ceará were assigned to Bahia and almost all specimens misidentified in Bahia were classified as Ceará), so samples were pooled in the northern and south‐eastern samples, and Rio Grande do Sul was considered a southern area. Eight parasite species were characteristic of the northern localities, five species were found just in the area associated with south‐eastern localities and two species were characteristic of the southern area providing first evidence of stock discreteness. The multivariate discriminant analysis successfully discriminated three groups of localities associated with three stocks of M. furnieri in Brazil: a northern stock associated with Ceará and Bahia, a south‐eastern stock related to Rio de Janeiro and Santa Catarina and a southern stock in the area of Rio Grande do Sul, which could be considered as the northern limit of the stock associated with the Common Fishing Zone of Uruguay and Argentina.     

Geographic differentiation of <Emphasis Type="Italic">Cobitis shikokuensis</Emphasis> inferred from mtDNA RFLP analysis

Mitochondrial DNA divergence among populations of the Japanese spinous loach Cobitis shikokuensis, endemic to Shikoku Island, was investigated by restricted fragment length polymorphism analysis. A total of 68 restriction sites on DNA fragments from the cytochrome b to D-loop regions and from the 12S rRNA to 16S rRNA regions, amplified by PCR, were analyzed. A total of 12 haplotypes (plus 6 in outgroups) were detected in 268 specimens collected from 19 localities in seven rivers (and 41 specimens from four localities in three rivers in outgroups). Three of the seven river populations of C. shikokuensis were shown to have unique haplotypes, and four of the seven river populations were monomorphic. The nested structure of the haplotype network for populations of C. shikokuensis exhibited two large clades corresponding to (1) populations from the Shimanto River and its neighbors and (2) two genetically divergent populations in the Shigenobu and Iwamatsu Rivers. The population from the Shimanto River, the largest river inhabited by C. shikokuensis, maintains great haplotype diversity as well as the allozyme diversity previously reported. On the other hand, populations from the Hiji River, the second largest river, which exhibited the highest allozyme diversity, were monomorphic in their mtDNA. The nested clade analysis (NCA) revealed that past fragmentation between the above two clades could occur in the initial distribution process of C. shikokuensis. The large genetic divergence of two river populations from the Shigenobu and Iwamatsu Rivers was inferred to be caused by a process of long distance colonization and fragmentation. MtDNA introgression into the Hiji River population from southern river populations was suggested. Taking genetic divergence into consideration, each river population of C. shikokuensis should be conserved separately as like a distinct species, and conservation programs for the small populations showing less genetic variability should be invoked as soon as possible.     

A new species of spiny driftwood catfish Spinipterus (Siluriformes: Auchenipteridae) from the Amazon basin

An expedition to the middle Rio Purus basin uncovered a remarkable new species of the genus Spinipterus. The new species has a very distinct and conspicuous colour pattern resembling a jaguar and it is almost four times larger than Spinipterus acsi, a small specimen (32 mm L_S) from Caño Santa Rita, a right bank tributary of Río Nanay in Peru and a second specimen was reported from Rio Juruá, Amazonas State, Brazil. Although the new species is more similar in size and colour pattern to Liosomadoras, it shares the synapomorphies for Spinipterus. The new species differs from the congener by the following characters: (a) colour pattern with large black rosette-like spots over a light yellow to brown background (v. brown background with small dark blotches over the body); (b) adult body size reaching 104.5 mm L_S (v. maximum known size 37.1 mm L_S); (c) posterior process of cleithrum short, never reaching vertical through the dorsal-fin origin (v. posterior process long, surpassing vertical through the dorsal-fin origin); (d) seven soft pectoral-fin rays (v. six); (e) caudal fin truncated (v. caudal fin rounded).     

THE ROLE OF INTROGRESSIVE HYBRIDIZATION IN THE EVOLUTION OF THE GILA ROBUSTA COMPLEX (TELEOSTEI: CYPRINIDAE)

Abstract The extent and impact of introgressive hybridization was examined in the Gila robusta complex of cyprinid fishes using mitochondrial DNA (mtDNA) sequence variation. Lower Colorado River basin populations of G. robusta, G. elegans, and G. cypha exhibited distinct mtDNAs, with only limited introgression of G. elegans into G. cypha. The impact of hybridization was significant in upper Colorado River basin populations; most upper basin fishes sampled exhibited only G. cypha mtDNA haplotypes, with some individuals exhibiting mtDNA from G. elegans. The complete absence of G. robusta mtDNA, even in populations of morphologically pure G. robusta, indicates extensive introgression that predates human influence. Analysis of the geographic distribution of variation identified two distinctive G. elegans lineages; however, the small number of individuals and localities sampled precluded a comprehensive analysis. Analysis of haplotype and population networks for G. cypha mtDNAs from 15 localities revealed low divergence among haplotypes; however, significant frequency differences among populations within and among drainages were found, largely attributable to samples in the Little Colorado River region. This structure was not associated with G. cypha and G. robusta, as morphotypes from the same location are more similar than conspecific forms in other locations. This indicates that morphological and mtDNA variation are affected by different evolutionary forces in Colorado River Gila and illustrates how both hybridization and local adaptation can play important roles in evolution.     

INTRASPECIFIC PHYLOGEOGRAPHY OF NORTH AMERICAN HIGHLAND FISHES: A TEST OF THE PLEISTOCENE VICARIANCE HYPOTHESIS

The highland fish fauna of eastern North America consists of Appalachian and Ozark centers of endemism separated by the intervening Glacial Till Plains. Clades within these areas are more closely related phylogenetically to each other than to clades occurring in the intervening formerly glaciated region, suggesting that the Pleistocene glaciations fragmented a widespread highland region and its associated fauna. Alternatively, it is possible that these faunal assemblages predate the glaciations or that recent dispersals may have been more important than vicariance in determining faunal compositions. We examined the relationships among mitochondrial DNA (mtDNA) haplotypes within five clades of highland fishes, each with a distribution suggestive of a Pleistocene vicariance event. Darters of the subgenera Litocara and Odontopholis have distributions and mtDNA relationships that are consistent with the Pleistocene integration and burial of the Teays-Mahomet valley, a major drainage of the early Pleistocene. The distribution and mtDNA relationships among subspecies of Erimystax dissimilis are not consistent with Pleistocene vicariance, but relationships among Appalachian haplotypes are consistent with the late Pleistocene integration of the modern Ohio River system. Both Cottus carolinae and the Fundulus catenatus species group have representatives in the Mobile basin consistent with pre-Pleistocene divergences. Three haplotype clusters were found in C. carolinae, corresponding to the Appalachian, Ozark, and upper Kanawha River populations. However, Appalachian and Ozark F. catenatus populations are paraphyletic with respect to each other. This, coupled with a relatively low degree of sequence divergence, suggests that no long-term barriers to gene flow exist for C. carolinae and F. catenatus. These three distinct phylogeographic patterns indicate that Pleistocene vicariance is not the only explanation for the Appalachian-Ozark distribution of highland fish communities.     

Inter‐basin exchange and repeated headwater capture across the Sierra Madre Occidental inferred from the phylogeography of Mexican stonerollers

Aim Geomorphic evolution of river basins can shape the structure and diversity of aquatic communities, but understanding the biological significance of basin evolution can be challenging in semi‐arid regions with ephemeral or endorheic conditions and complex drainage configurations such as the Sierra Madre Occidental (SMO) in North America. In this study, we characterized range‐wide patterns of genetic variation in the Mexican stoneroller (Campostoma ornatum) to infer how orogenic and erosional influences on river basin connectivity have given rise to the diverse and largely endemic freshwater communities across the SMO region. Location Twelve drainage basins across northern Mexico and the south‐western United States, centred on the SMO. Methods  We collected 202 specimens from 98 localities across the range of C. ornatum. We performed phylogenetic analyses of DNA sequences from one mitochondrial (cytochrome b) and one nuclear (intron S7) gene. Phylogenetic trees were estimated for each data set using maximum likelihood and Bayesian inference. Results Phylogenetic analyses consistently resolved a monophyletic C. ornatum composed of multiple evolutionary lineages within two markedly divergent clades that differentiate northern drainages from southern drainages in the SMO region. Within‐clade patterns of divergence corresponded to fine‐scale geographic structure within and among SMO drainage basins. However, the geographic distribution of evolutionary lineages within the northern and southern clades did not always correspond to the geographic configuration of drainage basins. Some subclades encompassed multiple drainages, and individuals from a single drainage were sometimes recovered in multiple subclades. Main conclusions Our findings indicate that a common ancestor of Mexican Campostoma is likely to have entered north‐west Mexico through an ancient Rio Grande system that extended as far south as the Rio Nazas and Rio Aguanaval. The geographic orientation of the two strongly divergent clades recovered within C. ornatum provides evidence of long‐standing isolation of southern basins from northern basins within the ancestral Rio Grande system, possibly due to the combined influence of tectonic events and increasing regional aridity. Geographic patterns of genetic variation also provide evidence of range expansion from Atlantic to Pacific drainages due to drainage evolution and river capture events, as well as further inter‐basin exchange via more recent headwater capture events, hydrological connections and possible anthropogenic introductions.     

Genetic variation in the stygobitic shrimp Creaseria morleyi (Decapoda: Palaemonidae), evidence of bottlenecks and re‐invasions in the Yucatan Peninsula

The karstic nature of the Yucatan Peninsula promotes the formation of submerged caves and sinkholes that are inhabited by an endemic subterranean water fauna. By contrast with most other micro‐endemic stygobitic species, the freshwater palaemonid shrimp Creaseria morleyi is widely distributed across the northern part of the peninsula. In the present study, we investigated the phylogeographic structure of C. morleyi using two mitochondrial genes as markers, and explored hypotheses related to its evolution in the peninsula. DNA from 14 localities was extracted, and the 16S rRNA and cytochrome oxidase subunit I (COI) genes were amplified and sequenced. The different haplotypes were identified to construct a haplotype network and perform a nested clade analysis. Five haplotypes of the 16S gene were obtained, with a maximum divergence of 0.5%. One of these haplotypes is widely distributed and the most divergent is located in the north‐western section of the peninsula. Twelve haplotypes for the COI gene were found with a maximum divergence of 2%, showing the same spatial pattern. The analysis revealed two significantly different clades corresponding to populations in the centre and south‐east of the peninsula as a consequence of restricted genetic flow with isolation‐by‐distance. The divergence time of these two clades was 40–120 thousand years. The genetic variation in C. morleyi, the relationship between haplotypes and their geographic distribution, along with the geological history of the Yucatan Peninsula, may indicate that this variation is a relict of an ancient marked genetic structure reduced by changes in sea level that resulted in a series of bottlenecks. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 315–325.     

Genetic differentiation in the Trinidad endemic Mannophryne trinitatis (Anura: Aromobatidae): Miocene vicariance,in situ diversification and lack of geographical structuring across the island

Trinidad offers a unique study system within the Caribbean to assess the processes and patterns of amphibian speciation. We used mitochondrial DNA sequences to investigate the phylogenetic relationships and patterns of intraspecific genetic variation of Mannophryne trinitatis from Trinidad. Molecular clock estimates point to a genetic split between M. trinitatis and its sister species, M. venezuelensis, dating to the Late Miocene (c. 7–8 Mya), suggesting vicariance as a means of speciation when Trinidad pulled apart from northern Venezuela. M. trinitatis phylogenetic population analyses from ten Northern Range and four Central Range localities recovered three well‐resolved clades: a larger clade formed by haplotypes from Northern Range localities and two additional clades, one formed by haplotypes from the Central Range and another including haplotypes from Northern Range localities and one haplotype from the Central Range. Overall, our results show that the genetic diversity in M. trinitatis is not geographically structured but it is distributed among the various Northern and Central Range localities. In congruence with the vicariance speciation hypothesis, we attribute M. trinitatis present distribution and lack of genetic structure to multiple admixture events caused by climate changes that severely affected the topology of Trinidad throughout the Pliocene/Pleistocene periods.     

Molecular signature of the D-loop in the brown pencilfish Nannostomus eques (Characiformes, Lebiasinidae) reveals at least two evolutionary units in the Rio Negro basin, Brazil

The genetic variability of the brown pencilfish Nannostomus eques was studied, based on an analysis of sequences from the control region (1084 bp) of mitochondrial (mt)DNA in 125 individuals collected from eight tributaries along the upper (Açaituba, Miuá, Jaradi and Arixanã), middle (Demini), and lower (Jacundá, Maguari and Catalão) Rio Negro (Brazil). Phylogenetic inferences using mtDNA data from N. eques revealed two evolutionary units. Genetic distance between them ranged from 5·5 to 8·3% and differed by 8·5–11·8% from the sister species pencilfish Nannostomus unifasciatus. The time of divergence between the two evolutionary units was estimated to be the Middle Pliocene (c. 2·99 million years before present). Population genetic analysis (DNA polymorphism, AMOVA and Mantel test) showed high haplotype diversity (HD, >0·90) in each evolutionary unit, a strong population genetic structure in the Demini River that formed a monophyletic group and a correlation between genetic divergence and geographical distance in only one of these units (evolutionary unit 1). On the basis of molecular data, the rapids and waterfalls near São Gabriel da Cachoeira (Upper Rio Negro) were the main barriers to gene flow within evolutionary unit 1 in some localities. The emergences of the Branco River and the Anavilhanas Archipelago were apparently responsible for the discrepancy in distribution of the two evolutionary units, except at Jacundá, where the evolutionary units were sympatric. In view of the differences between the evolutionary units, N. eques cannot be treated as a single stock in the Rio Negro basin. These results may have important implications for the fishery management of this ornamental fish.     

Phylogeography of the pallid kangaroo mouse,Microdipodops pallidus: a sand‐obligate endemic of the Great Basin,western North America

Aim Kangaroo mice, genus Microdipodops Merriam, are endemic to the Great Basin and include two species: M. pallidus Merriam and M. megacephalus Merriam. The pallid kangaroo mouse, M. pallidus, is a sand‐obligate desert rodent. Our principal intent is to identify its current geographical distribution and to formulate a phylogeographical hypothesis for this taxon. In addition, we test for orientation patterns in haplotype sharing for evidence of past episodes of movement and gene flow. Location The Great Basin Desert region of western North America, especially the sandy habitats of the Lahontan Trough and those in south‐central Nevada. Methods Mitochondrial DNA sequence data from portions of three genes (16S ribosomal RNA, cytochrome b, and transfer RNA for glutamic acid) were obtained from 98 individuals of M. pallidus representing 27 general localities sampled throughout its geographical range. Molecular sequence data were analysed using neighbour‐joining, maximum‐parsimony, maximum‐likelihood and Bayesian methods of phylogenetic inference. Directional analysis of phylogeographical patterns, a novel method, was used to examine angular measurements of haplotype sharing between pairs of localities to detect and quantify historical events pertaining to movement patterns and gene flow. Results Collecting activities showed that M. pallidus is a rather rare rodent (mean trapping success was 2.88%), and its distribution has changed little from that determined three‐quarters of a century ago. Two principal phylogroups, distributed as eastern and western moieties, are evident from the phylogenetic analyses (mean sequence divergence for cytochrome b is c. 8%). The western clade shows little phylogenetic structure and seems to represent a large polytomy. In the eastern clade, however, three subgroups are recognized. Nine of the 42 unique composite haplotypes are present at two or more localities and are used for the orientation analyses. Axial data from haplotype sharing between pairwise localities show significant, non‐random angular patterns: a north‐west to south‐east orientation in the western clade, and a north‐east to south‐west directional pattern in the eastern clade. Main conclusions The geographical range of M. pallidus seems to be remarkably stable in historical times and does not show a northward (or elevationally upward) movement trend, as has been reported for some other kinds of organism in response to global climate change. The eastern and western clades are likely to represent morphologically cryptic species. Estimated times of divergence of the principal clades of M. pallidus (4.38 Ma) and between M. pallidus and M. megacephalus (8.1 Ma; data from a related study) indicate that kangaroo mice diverged much earlier than thought previously. The phylogeographical patterns described here may serve as a model for other sand‐obligate members of the Great Basin Desert biota.     

Streaked horned lark <Emphasis Type="Italic">Eremophila alpestris strigata</Emphasis> has distinct mitochondrial DNA

The Streaked Horned Lark (STHL; Eremophila alpestris strigata) is a federal candidate for listing under the Endangered Species Act. We evaluated the conservation status and level of genetic diversity of the STHL using the complete mitochondrial ND2 gene. We sampled 32 STHLs from the southern Puget Sound region, the Pacific coast, and Whites Island in the Columbia River of Washington, and additional 68 horned larks from Alaska, alpine and eastern Washington, Oregon, California, and Asia (outgroups). Our Maximum Likelihood analysis of 32 haplotypes identified three geographically concordant clades in Pacific coast states: Pacific Northwest (alpine and eastern Washington, Alaska), Pacific Coast (western Washington, California), and Great Basin (eastern Oregon). Each of the three clades was supported by bootstrap values ≥86%. The distance among them varied from 0.72 to 0.79% nucleotide divergence excluding intraclade variation. The relationship among the clades was not resolved. AMOVA also showed significant structuring of haplotypes among the three clades. Differences among clades accounted for 75.7% of sequence variation, differences among localities within clades accounted for 12.1%, and differences among individuals within localities accounted for the remaining 12.2%. Although STHL populations were closely related to the Californian sample, they appeared unique and isolated. All pairwise F _st values involving the STHL samples were significant (except between themselves). STHLs appear to have remarkably low genetic diversity; all 32 STHLs shared the same haplotype. Even with small sample sizes, all other localities had multiple haplotypes. Because the STHL appears to be unique and isolated, and to have little genetic diversity our data suggest it should be a conservation priority.