Phylogeography of Sylvirana latouchii (Anura, Ranidae) in Taiwan

Biogeographic studies are important for understanding the natural history of faunas. To comprehend the geographical patterns of genetic variation in anurans in Taiwan, we investigated the genetic structure of Sylvirana latouchii (Anura, Ranidae) from 31 populations by using mitochondrial DNA (mtDNA) cytochrome b sequences. A neighbor-joining tree of 38 haplotypes revealed three major divergences in Taiwanese S. latouchii: the northern, western, and eastern-and-southern clades. Each clade was restricted to a single geographical district and showed obvious differentiation. The patterns of geographical divergence in this species reflect common historical events experienced by other native animals distributed in Taiwan. The order of divergence times between clades was inferred using a molecular clock test. The population relationship of S. latouchii between Taiwan and mainland China is discussed. Further study employing more populations of S. latouchii from mainland China is necessary to clarify the original geographical patterns and migratory history of this species.     

从线粒体基因探讨中国大头蛙群的分类及其属内地位

Partial sequences of the mitochondrial 12S rRNA and 16S rRNA gene were determined for 8 populations of three species of Chinese Limnonectes, and aligned with the published sequences of Limnonectes from other parts of the world. When Nanorana parker, Paa boulengeri, Fejervarya limnocharis and Hoplobatrachus rugulosus was used as outgroup taxa (Accession Nos. AY158705, AY313685, AF206111, AF206491, AY322311). The sequences of the 12S rRNA and 16S rRNA genes totaled 950 nueleotide positions with gaps including 510 variable sites. We reconstructed phylogenetie trees using Clustal X 1.8, Mega 2.1 and PHYLIP 3.5e software, and using the maximum parsimony and maximum likelihood methods, respectively. Our analyses suggest that these fanged frogs from China are another monophyletie group in addition to the four monophyletie groups identified by previous studies. The Chinese Limnonectes were grouped into three elades (BCL 55% ). The first elade contains one species (BCL 100% ), from a population of Limnoneetes fragilis from Hainan Province. The second contains four individuals (BCL 100% ), i. e. two populations of Limnonectes kuhlii from Yunnan Province. The third contains one species (BCL 100% ), i. e. five populations of Limnonectes fujianensis from Fujian Province and 1 from Taiwan Province. The resulted phylogenetie trees indicate L. fragilis is basal to L. kuhlii L. fujianensis 。     

Phylogenetic relationships of rat lungworm, Angiostrongylus cantonensis, isolated from different geographical regions revealed widespread multiple lineages

We conducted a pilot survey of genetic variation of A. cantonensis using small subunit (SSU) ribosomal (r) RNA and mitochondrial cytochrome c oxidase subunit I (coxI) gene sequences. Two distinct SSU genotypes (G1 and G2) were identified among 17 individual A. cantonensis worms from 17 different geographical localities in Japan, Mainland China, Taiwan, and Thailand. The partial coxI sequences were determined for 83 worms from 18 different geographical localities from Japan, Mainland China, Taiwan, and Thailand. Phylogenetic analysis showed eight distinct coxI haplotypes (ac1 to ac8). In 16 out of 18 localities, only a single coxI haplotype was found. However, in two localities, two coxI haplotypes coexisted. The common haplotypes found were: haplotype ac1 (Tokyo, Chiba, Kanagawa, Amamioshima Island, and Taichung), haplotype ac2 (Ishikawa, Shenzhen, and Lianjiang), haplotype ac5 (the Okinawa and the Ogasawara Islands), and haplotype ac7 (Miyagi, Aichi, and Kanagawa). Each of these regions is separated from the others by high mountain ranges or oceans. In addition, the lower genetic variation and particular geographical distribution of A. cantonensis in each location could indicate a founder effect, which may have resulted from multiple independent origins, and suggests that haplotypes migrated from endemic areas via human-related transportation.     

DNA barcoding reveals cryptic diversity in the peanut worm Sipunculus nudus

Peanut worm (Sipunculus nudus) is a cosmopolitan species mainly distributed in tropical and subtropical coastal waters. Analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences among S. nudus from GenBank revealed high genetic variation (p‐distance, 0.115–0.235; k2p, 0.128–0.297) and paraphyletic relationships. These indicated misidentification and/or cryptic diversity may be present in the genus Sipunculus. To understand the genetic diversity and to manage the recourse of S. nudus, we collected specimens from coastal waters of southern China and Taiwan. In the phylogenetic topology, specimens can be separated into four distinct clades; three of these clades (clade A, B and C) were only represented from this region (southern China and Taiwan), but the clade D grouped with individuals from Central America (Atlantic coast). Furthermore, individuals of clades A and D were collected at the same location, which does not support the hypothesis that this genetic break reflects contemporary geographical isolation. The four distinct clades observed among coastal waters of southern China and Taiwan indicated underestimated diversity. It is noteworthy that the cryptic diversity is vulnerable under high pressure of human activity.     

斑衣蜡蝉若虫寄生蜂地理种群遗传差异及早期快速检测

【目的】明确不同地理种群斑衣蜡蝉Lycorma delicatula若虫寄生蜂种群遗传差异,实现若虫被寄生早期的快速准确检测,以评估其对斑衣蜡蝉种群的控制作用。【方法】利用DNA条形码技术获得不同地理种群斑衣蜡蝉若虫寄生蜂COI和28S rDNA序列,利用K2P模型计算不同地理种群间的遗传距离,以邻接(neighbor-joining,NJ)法构建系统发育树;基于COI序列设计种特异性PCR(SS-PCR)引物,利用SS-PCR对斑衣蜡蝉若虫DNA进行扩增,测定其体内是否有中华螯蜂Dryinus sinicus寄生;利用目测法观察和PCR扩增测定寄生蜂对不同采样点斑衣蜡蝉若虫的寄生率。【结果】经鉴定,不同地理种群斑衣蜡蝉若虫寄生蜂为中华螯蜂,该寄生蜂COI序列共检测到16个单倍型,28S rDNA序列共检测到4个单倍型。不同地理种群间中华螯蜂遗传距离在0.00691~0.01310之间。邻接法构建的系统发育树显示不同地理种群中华螯蜂均聚于一枝。基于COI序列设计的SS-PCR引物对中华螯蜂成虫、幼虫均具有良好的扩增效果,最低检测阈值为0.000005 ng/μL DNA。利用SS-PCR测定中华螯蜂对各采样点斑衣蜡蝉若虫的寄生率为22.54%~60.00%,显著高于目测统计的结果(5.63%~36.98%)。【结论】不同中华螯蜂地理种群间遗传差异较小;SS-PCR引物可用于不同地区中华螯蜂对斑衣蜡蝉早期寄生率的快速检测。     

The Phylogeographical Pattern and Conservation of the Chinese Cobra (Naja atra) across Its Range Based on Mitochondrial Control Region Sequences

The vulnerable Chinese cobra (Naja atra) ranges from southeastern China south of the Yangtze River to northern Vietnam and Laos. Large mountain ranges and water bodies may influence the pattern of genetic diversity of this species. We sequenced the mitochondrial DNA control region (1029 bp) using 285 individuals collected from 23 localities across the species'' range and obtained 18 sequences unique to Taiwan from GenBank for phylogenetic and population analysis. Two distinct clades were identified, one including haplotypes from the two westernmost localities (Hekou and Miyi) and the other including haplotypes from all sampling sites except Miyi. A strong population structure was found (Φst = 0.76, P<0.0001) with high haplotype diversity (h = 1.00) and low nucleotide diversity (π = 0.0049). The Luoxiao and Nanling Mountains act as historical geographical barriers limiting gene exchange. In the haplotype network there were two “star” clusters. Haplotypes from populations east of the Luoxiao Mountains were represented within one cluster and haplotypes from populations west of the mountain range within the other, with haplotypes from populations south of the Nanling Mountains in between. Lineage sorting between mainland and island populations is incomplete. It remains unknown as to how much adaptive differentiation there is between population groups or within each group. We caution against long-distance transfers within any group, especially when environmental differences are apparent.     

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.     

中国大头蛙属3个种线粒体ND1基因全序列分析与亲缘关系

测定了大头蛙和脆皮大头蛙线粒体ND1基因全序列长度分别为978 bp和958 bp,(对应编码325和319个氨基酸)。对所测基因序列组分进行了分析,并与福建大头蛙同源序列进行比较发现,978个核苷酸位点中,有664个保守位点和多变位点294个。同时发现福建大头蛙与大头蛙该基因序列的同源性最高(核苷酸序列同源性为78.77%,氨基酸序列为92.62%)。基于ND1基因全序列的氨基酸和核苷酸两种数据形式,选用M ega3.1软件中的NJ法对大头蛙属3个种、黑斑蛙、泽陆蛙及外群中国大鲵共6条基因序列进行系统树重建分析,结果表明:所得的2个NJ树均将大头蛙属3个种聚于一支,其中大头蛙与福建大头蛙为姐妹群关系(自检值均高度支持),从而证实了大头蛙与福建大头蛙亲缘关系较近的观点。     

Strong population genetic structure of an invasive species,Rhynchophorus ferrugineus (Olivier), in southern China

The red palm weevil (RPW), Rhynchophorus ferrugineus (Olivier), was initially reported in China in the 1990s and is now considered one of the most successful invasive pests of palm plants in the country. A total of 14 microsatellite loci and one mitochondrial cytochrome oxidase subunit Ι (cox I) gene fragment were used to investigate the genetic characteristics and structure of R. ferrugineus in southern China. High levels of genetic differentiation among populations and significant correlations between genetic and geographical distances indicated an important role of geographical distance in the distribution of the RPW in southern China. High gene flow between Fujian and Taiwan province populations illustrated the increased effects of frequent anthropogenic activities on gene flow between them. Genetic similarity (i.e., haplotype similarity) indicated that RPW individuals from Taiwan and Fujian invaded from a different source than those from Hainan. To some extent, the genetic structure of the RPW in southern China correlated well with the geographic origins of this pest. We propose that geographical distance, anthropogenic activities, and the biological attributes of this pest are responsible for the distribution pattern of the RPW in southern China. The phylogenetic analysis suggests that the most likely native sources of the RPW in southern China are India, the Philippines, and Vietnam.     

Multilocus phylogeny of a cryptic radiation of Afrotropical long-fingered bats (Chiroptera,Miniopteridae)

The Old World bat family Miniopteridae comprises only the genus Miniopterus, which includes 20 currently recognized species from the Afrotropical realm and 15 species from Eurasia and Australasia. Since 2003, the number of recognized Miniopterus species has grown from 19 to 35, with most newly described species endemic to Madagascar and the Comoros Archipelago. We investigated genetic variation, phylogenetic relationships and clade membership in Miniopterus focusing on Afrotropical taxa. We generated mitochondrial cytochrome-b (cyt-b) and nuclear intron data (five genes) from 352 vouchered individuals collected at 78 georeferenced localities. Including 99 additional mitochondrial sequences from GenBank, we analysed a total of 25 recognized species. Mitochondrial genetic distances among cyt-b-supported clades averaged 9.3%, representing as many as five undescribed species. Multilocus coalescent delimitation strongly supported the genetic isolation of eight of nine tested unnamed clades. A large number of sampled clades in sub-Saharan Africa are distributed wholly or partly in East Africa (nine of 13 clades), suggesting that Miniopterus diversity has been grossly underestimated. Although 25 of 27 cyt-b and 23 of 25 nuclear gene tree lineages from the Afrotropics were strongly supported as monophyletic, a majority of deep nodes were poorly resolved in phylogenetic analyses. Long terminal branches subtending short backbone internodes in the phylogenetic analyses suggest a rapid radiation model of diversification. This hypothesis needs to be tested using more phylogenetically informative data.     

Phylogenetic relationships and biogeography of the Japanese clawed salamander, Onychodactylus japonicus (Amphibia: Caudata: Hynobiidae), and its congener inferred from the mitochondrial cytochrome b gene

Using the mitochondrial cytochrome b gene, we investigated phylogenetic relationships between and within the Japanese clawed salamander, Onychodactylus japonicus, and its close continental relative O. fischeri. Monophyly of O. japonicus was well supported, and O. japonicus was clearly distinguished from O. fischeri. However, O. fischeri comprises genetically distinct populations from Russia, NE China, and Korea that do not form a monophyletic group. Within O. japonicus, four major clades were clearly recognized: Clade I from northern Tohoku district, Clade II from southern Tohoku district and the Tsukuba Mountains, Clade III from southwestern Honshu, and Clade IV from Kinki and Chugoku districts in Honshu and from Shikoku. Although genetic distances among these clades were large (5.5-9.6%), relationships among the clades were unresolved. All clades except Clade I contained two or three distinct subclades. In several localities in Kinki and Chugoku, Clades III and IV were sympatric. The estimated divergence times and available geohistorical data suggest that O. japonicus began to differentiate in the Upper Late Miocene and that the pattern of genetic differentiation of this species has been affected strongly by climate changes and geohistorical events such as volcanic activity and mountain formation. Our results suggest that both O. fischeri and O. japonicus comprise multiple cryptic species.     

Cryptic diversification of the swamp eel Monopterus albus in East and Southeast Asia, with special reference to the Ryukyuan populations

The swamp eel Monopterus albus is widely distributed in tropical and subtropical freshwaters ranging from Southeast Asia to East Asia, and is unique in its ability to breathe air through the buccal mucosa. To examine the genetic structure of this widespread species, molecular phylogenetic analyses of mitochondrial 16S rRNA sequence (514 bp) were conducted for 84 specimens from 13 localities in Southeast and East Asia. The analyses showed clearly that this species can be genetically delineated into three clades based on geographical populations [China–Japan (Honshu + Kyushu), Ryukyu Islands, and Southeast Asia clades], with each clade exhibiting its own reproductive behavior. Therefore, “M. albus” is believed to be composed of at least three species. The Southeast Asia clade with the highest genetic diversity may include more species. The Ryukyu clade was estimated to have diverged more than 5.7 million years ago, suggesting that the Ryukyuan “M. albus” is native. In contrast, in the China–Japan clade, all haplotypes from Japan were closely related to those from China, suggesting artificial introduction(s).     

基于线粒体COI基因序列的大豆食心虫中国东北地理种群遗传多样性分析

【目的】大豆食心虫Leguminivora glycinivorella (Matsumura)是一种危害大豆的主要害虫,在中国北方地区危害较重。本研究旨在探讨大豆食心虫在中国东北不同地理种群间的遗传变异。【方法】测定了10个不同地理种群153个个体的线粒体细胞色素氧化酶亚基Ⅰ (mtCOI)基因的657 bp序列,利用DnaSP 5. 0和Arlequin 3. 5. 1. 2等软件对大豆食心虫种群间的遗传多样性、基因流水平和分子变异进行分析。【结果】结果表明：10个地理种群间的COI基因共有36个变异位点和17个单倍型,其中1个单倍型为10个种群所共享。总种群的单倍型多样性指数Hd为0.456,各地理种群单倍型多样度范围在0~0.634之间。总群体的固定系数Fst为0.12545,遗传分化系数Gst为0.06326,总基因流Nm为3.49,且各种群间的基因流均大于1,种群间基因交流的水平较高。【结论】大豆食心虫种群内遗传多样性水平处于中低等水平。总群体和各种群的Tajima’s D检验结果皆不显著,说明中国东北地区大豆食心虫在较近的历史时期内没有出现种群扩张现象。AMOVA分子变异分析结果表明,大豆食心虫的遗传分化主要来自种群内部,而种群间未发生明显的遗传分化。各地理种群的单倍型在系统发育树上和中介网络图上散布在不同的分布群中,缺乏明显的地理分布格局。各种群的遗传距离与地理距离之间没有显著线性相关性,种群间的基因交流并未受到地理距离的影响。     

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 relationships within the pan-oriental narrow-mouth toad Microhyla ornata as revealed by mtDNA analysis (Amphibia, Anura, Microhylidae)

A molecular phylogenetic survey was conducted using mtDNA sequences of 12S and 16S rRNA, and cyt-b genes to examine taxonomic relationships among populations of the Pan-Oriental microhylid, Microhyla ornata, from India, Bangladesh, Thailand, Laos, China, Taiwan, and the Ryukyu Archipelago of Japan. Two discrete clades are recognized within this species, one consisting of populations from India and Bangladesh, and the other encompassing the remaining populations. In the latter clade, populations from the Ryukyu Archipelago are clearly split from the rest (populations from Taiwan and the continent) with considerable degrees of genetic differentiations. Each of the three lineages is judged to represent a good species, and the name Microhyla ornata is restricted to the South Asian populations. For the populations from Taiwan and a wide region from China to Southeast Asia, the name Microhyla fissipes should be applied, whereas the Ryukyu populations are most appropriately referred to as Microhyla okinavensis, although further substantial genetic differentiations are recognized among some island group populations within this last species.     

Mitochondrial phylogeography of the Dalmatian wall lizard, Podarcis melisellensis (Lacertidae)

A 903 bp section of the mitochondrial cytochrome b gene was sequenced from 73 specimens of Podarcis melisellensis collected at 52 localities distributed over the major part of the species’ range. In addition, parts of the 12S (about 470 bp) and 16S rRNA (about 500 bp) genes were analysed for 11 representative samples leading to a congruent phylogeny. Our study includes representatives of all 20 subspecies recognized today. The phylogenetic analysis of the sequence data revealed three main clades: mainland with nearby islands, Vis archipelago, and Lastovo archipelago. The degree of mitochondrial DNA divergence among these clades suggests a separation of the respective population groups during the earliest Pleistocene. The phylogenetic pattern observed within the species is in sharp contrast to the actual taxonomic division into subspecies. A correlation between genetic diversity of P. melisellensis populations and paleogeography of the regions they inhabit is discussed.     

Distinct Genetic Diversity of Oncomelania hupensis,Intermediate Host of Schistosoma japonicum in Mainland China as Revealed by ITS Sequences

Background

Oncomelania hupensis is the unique intermediate host of Schistosoma japonicum, which causes schistosomiasis endemic in the Far East, and especially in mainland China. O. hupensis largely determines the parasite''s geographical range. How O. hupensis''s genetic diversity is distributed geographically in mainland China has never been well examined with DNA sequence data.

Methodology/Principal Findings

In this study we investigate the genetic variation among O. hupensis from different geographical origins using the combined complete internal transcribed spacer 1 (ITS1) and ITS2 regions of nuclear ribosomal DNA. 165 O. hupensis isolates were obtained in 29 localities from 7 provinces across mainland China: lake/marshland and hill regions in Anhui, Hubei, Hunan, Jiangxi and Jiangsu provinces, located along the middle and lower reaches of Yangtze River, and mountainous regions in Sichuan and Yunnan provinces. Phylogenetic and haplotype network analyses showed distinct genetic diversity and no shared haplotypes between populations from lake/marshland regions of the middle and lower reaches of the Yangtze River and populations from mountainous regions of Sichuan and Yunnan provinces. The genetic distance between these two groups is up to 0.81 based on Fst, and branch time was estimated as 2–6 Ma. As revealed in the phylogenetic tree, snails from Sichuan and Yunnan provinces were also clustered separately. Geographical separation appears to be an important factor accounting for the diversification of the two groups of O. hupensis in mainland China, and probably for the separate clades between snails from Sichuan and Yunnan provinces. In lake/marshland and hill regions along the middle and lower reaches of the Yangtze River, three clades were identified in the phylogenetic tree, but without any obvious clustering of snails from different provinces.

Conclusions

O. hupensis in mainland China may have considerable genetic diversity, and a more complex population structure than expected. It will be of significant importance to consider the genetic diversity of O. hupensis when assessing co-evolutionary interactions with S. japonicum.     

Mitochondrial DNA sequence variation and phylogeography among Salmo trutta L. (Greek brown trout) populations

To investigate the phylogenetic relationships and geographical structure among brown trout S. trutta L. populations from the South Adriatic-Ionian and Aegean sea basins, mitochondrial DNA nucleotide sequence comparisons were used. A 310-base-pair (bp) segment of the control region (D-loop), and an additional 280-bp segment of the cytochrome b gene were sequenced from representatives of 13 brown trout populations. Phylogenetic analyses, conducted after combining the data presented with published data from other Eurasian brown trout, revealed four major phylogenetic groups, three of which were found widely distributed within the southern Balkan region. The phylogeographical patterns revealed by mtDNA represent one of the few cases where phylogenetic discontinuity in a gene tree exists without obvious geographical localization within a species' range and has most likely resulted from the differentiation of the major mtDNA clades during Messinian or early Pleistocene times. Finally, the genetic relationships among the populations suggested by mtDNA were generally not in accordance with either allozyme or morphological data.     

A phylogeny of the Tylototriton asperrimus group (Caudata: Salamandridae) based on a mitochondrial study: suggestions for a taxonomic revision

A phylogenetic hypothesis for the Asian newts of the Tylototriton asperrimus group was generated using data from two mitochondrial fragments including COI and the ND1-ND2 regions. Four distinct clades (A, B, C, D) were resolved with high nodal support within this monophyletic group. Clade A included T. asperrimus, T. hainanensis, T. notialis, "T. vietnamensis", and two unnamed salamander populations from Vietnam. Clade A, constituted the sister group of clades B + C. Newly identified clade C likely represents a new cryptic species. Clade C was the sister group of T. wenxianensis. The true T. vietnamensis exclusively constituted clade D. Our results bring into question some previous taxonomic decisions, and a revision is required. This study illustrates the necessity to include samples from type localities in taxonomic studies, and highlights the importance of fine-grained geographical sampling.     

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.