Genetic differentiation of the pine processionary moth at the southern edge of its range: contrasting patterns between mitochondrial and nuclear markers

The pine processionary moth (Thaumetopoea pityocampa) is an important pest of coniferous forests at the southern edge of its range in Maghreb. Based on mitochondrial markers, a strong genetic differentiation was previously found in this species between western (pityocampa clade) and eastern Maghreb populations (ENA clade), with the contact zone between the clades located in Algeria. We focused on the moth range in Algeria, using both mitochondrial (a 648 bp fragment of the tRNA‐cox2) and nuclear (11 microsatellite loci) markers. A further analysis using a shorter mtDNA fragment and the same microsatellite loci was carried out on a transect in the contact zone between the mitochondrial clades. Mitochondrial diversity showed a strong geographical structure and a well‐defined contact zone between the two clades. In particular, in the pityocampa clade, two inner subclades were found whereas ENA did not show any further structure. Microsatellite analysis outlined a different pattern of differentiation, with two main groups not overlapping with the mitochondrial clades. The inconsistency between mitochondrial and nuclear markers is probably explained by sex‐biased dispersal and recent afforestation efforts that have bridged isolated populations.     

Leopard tortoises in southern Africa have greater genetic diversity in the north than in the south (Testudinidae)

In contrast to mammals, little is known about the phylogeographic structuring of widely distributed African reptile species. With the present study, we contribute data for the leopard tortoise (Stigmochelys pardalis). It ranges from the Horn of Africa southward to South Africa and westwards to southern Angola. However, its natural occurrence is disputed for some southern regions. To clarify the situation, we used mtDNA sequences and 14 microsatellite loci from 204 individuals mainly from southern Africa. Our results retrieved five mitochondrial clades; one in the south and two in the north‐west and north‐east of southern Africa, respectively, plus two distributed further north. Using microsatellites, the southern clade matched with a well‐defined southern nuclear cluster, whilst the two northern clades from southern Africa corresponded to another nuclear cluster with three subclusters. One subcluster had a western and central distribution, another occurred mostly in the north‐east, and the third in a small eastern region (Maputaland), which forms part of a biodiversity hotspot. Genetic diversity was low in the south and high in the north of our study region, particularly in the north‐east. Our results refuted that translocations influenced the genetic structure of leopard tortoises substantially. We propose that Pleistocene climatic fluctuations caused leopard tortoises to retract to distinct refugia in southern and northern regions and ascribe the high genetic diversity in the north of southern Africa to genetic structuring caused by the survival in three refuges and subsequent admixture, whereas tortoises in the south seem to have survived in only one continuous coastal refuge.     

Molecular evidence of Pleistocene bidirectional faunal exchange between Europe and the Near East: the case of the bicoloured shrew (Crocidura leucodon, Soricidae)

We sequenced 1077 bp of the mitochondrial cytochrome b gene and 511 bp of the nuclear Apolipoprotein B gene in bicoloured shrew (Crocidura leucodon, Soricidae) populations ranging from France to Georgia. The aims of the study were to identify the main genetic clades within this species and the influence of Pleistocene climatic variations on the respective clades. The mitochondrial analyses revealed a European clade distributed from France eastwards to north-western Turkey and a Near East clade distributed from Georgia to Romania; the two clades separated during the Middle Pleistocene. We clearly identified a population expansion after a bottleneck for the European clade based on mitochondrial and nuclear sequencing data; this expansion was not observed for the eastern clade. We hypothesize that the western population was confined to a small Italo-Balkanic refugium, whereas the eastern population subsisted in several refugia along the southern coast of the Black Sea.     

Phylogenetic structure among pocket gopher populations,genus Thomomys (Rodentia: Geomyidae), on the Baja California Peninsula

We determined the phylogenetic relationships, population history, and hierarchical structure of genetic variation in pocket gophers distributed on the Baja California Peninsula (BCP), based on extensive geographic sampling. Using a fragment of the mitochondrial gene cytochrome b (cyt b), we found three latitudinal structured geographic clades (northern, central, and southern). The northern clade occurs in the border area of the USA and the north of BCP, the central clade occurs from the peninsular highlands through the Central Desert of Baja California, and the southern clade is distributed south of the San Ignacio Lagoon. AMOVA showed that genetic variation is higher among clades (64%) than within populations (18.1%). The deepest divergence among clades is very shallow (～300 000 years), which suggests that climatic changes during the Pleistocene or some inhospitable habitats have affected the structure of this group, rather than influences from older marine transgressions. Phylogenetic groups disclosed by our results do not coincide with the current infraspecific classification; therefore, we propose a change of epithet for BCP gophers (Thomomys nigricans) and a new subspecific taxonomic arrangement with four subspecies: Thomomys nigricans anitae, Thomomys nigricans martirensis, Thomomys nigricans nigricans, and Thomomys nigricans russeolus. © 2013 The Linnean Society of London     

Successful genotyping of microsatellites in the woolly mammoth

Genetic analyses using ancient DNA from Pleistocene and early Holocene fossils have largely relied on mitochondrial DNA (mtDNA) sequences. Among woolly mammoths, Mammuthus primigenius, mtDNA analyses have identified 2 distinct clades (I and II) that diverged 1-2 Ma. Here, we establish that microsatellite markers can be effective on Pleistocene samples, successfully genotyping woolly mammoth specimens at 2 loci. Although significant differentiation at the 2 microsatellite loci was not detected between 16 clade I and 4 clade II woolly mammoths, our results demonstrate that the nuclear population structure of Pleistocene species can be examined using fast-evolving nuclear microsatellite markers.     

Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications

We analysed phylogeography and population genetic variation across the range of the western pond turtle (Emys marmorata) using rapidly evolving mitochondrial and nuclear DNA sequence data. Nuclear DNA sequences from two unlinked introns displayed extremely low levels of variation, but phylogenetic analyses based on mtDNA recovered four well-supported and geographically coherent clades. These included a large Northern clade composed of populations from Washington south to San Luis Obispo County, California, west of the Coast Ranges; a San Joaquin Valley clade from the southern Great Central Valley; a geographically restricted Santa Barbara clade from a limited region in Santa Barbara and Ventura counties; and a Southern clade that occurs south of the Tehachapi Mountains and west of the Transverse Range south to Baja California, Mexico. An analysis of molecular variance (amova) based on regional hydrographic units revealed that populations from the Sacramento Valley north to Washington were virtually invariant, with no evidence of population substructure among northern river drainage basins. In other areas, E. marmorata contains considerable unrecognized variation, particularly in central and southern California and in northern Baja California, Mexico. Our northern clade is congruent with the distribution of the subspecies Emys marmorata marmorata (Washington-central California). However, no clade is congruent with the distribution of the southern subspecies Emys marmorata pallida from central California-Baja. Thus, recognition of the current subspecies split is not warranted, based on the available genetic evidence. Our amova and phylogenetic results, in conjunction with a growing comparative database for other codistributed aquatic taxa, confirm the occurrence of genetic breaks across the Tehachapi Mountains and Transverse Range bounding the southern end of the Great Central Valley, and point to southern California as a rich source of cryptic genetic variation.     

Inferring the roles of vicariance,climate and topography in population differentiation in Salamandra algira (Caudata,Salamandridae)

Integrating information from species occurrence data, environmental variables and molecular markers can provide valuable insights about the processes of population persistence and differentiation. In this study, we present the most comprehensive overview of the evolutionary history of the North African salamander Salamandra algira (Caudata, Salamandridae) to date, including analyses of climatic and topographical variables, and sequences of two mitochondrial and two nuclear DNA fragments, with a special focus on Algerian populations, under‐represented in previous studies. Coalescent‐based phylogenetic analyses of mtDNA data recover four well‐supported population groups corresponding to described subspecies, with a western clade including populations in north‐western Morocco (with two subclades corresponding to the subspecies tingitana and splendens), and an eastern clade including populations from north‐eastern Morocco (subspecies spelaea) and Algeria (subspecies algira). Inferred split times between major clades date back to the Miocene, with additional splits within each major clade in the Plio‐Pleistocene. Present climatic (aridity) and topographical factors account for geographical discontinuities across population groups and help identify potential areas of secondary contact between clades corresponding to the subspecies tingitana and splendens in the Rif mountains in Morocco. Niche analysis indicates the absence of phylogenetic signal in the use of environmental space in this species.     

Desert salt flats as oases for the spider Saltonia incerta Banks (Araneae: Dictynidae)

The deserts of southwestern North America have undergone dramatic changes over their recent geological history including large changes in size and connectivity during the Pleistocene glaciopluvial cycles. This study examines the population history of the rare spider Saltonia incerta, once thought to be extinct, to determine the role of past climatological events in shaping the structure of the species. This species is restricted to salt crusts of intermittent or dry lakes, streams or rivers in the desert southwest, a region that was much wetter during glacial periods. We examine the distribution and genetic variability of populations to test whether there is recent dispersal throughout the range of the species. Analyses of mitochondrial and nuclear DNA indicate significant population structure, with one major clade comprising New Mexico localities and one comprising California‐northern Baja California localities. Finer‐scale structure is evident within the California clade, although not all of the subclades are reciprocally monophyletic. However, isolation with migration analysis suggests that migration is very low to non‐existent. These results extend the known distribution of Saltonia, provide genetic evidence of strong isolation among localities within drainage basins and between drainage basins and provide a mechanistic understanding of population connectivity after the aridification of the American southwest. The implication is that although the species' distribution has been fragmented, populations have persisted throughout this area, suggesting that desert salt flats may have served as refugia for at least some terrestrial species.     

Colonization history of north European field voles (Microtus agrestis) revealed by mitochondrial DNA

The genetic structure of field vole (Microtus agrestis) populations from northern Europe was examined by restriction fragment length polymorphisms of mitochondrial DNA (mtDNA) in 150 individuals from 67 localities. A total of 83 haplotypes was observed, most of which were rare and highly localized geographically. Overall nucleotide diversity was high (134%), but showed a tendency to decrease with higher latitude. Two major mtDNA lineages differing by 2% in nucleotide sequence were identified. A southern mtDNA lineage was observed in field voles from Britain, Denmark and southern and central Sweden, whereas voles from Finland and northern Sweden belonged to a northern lineage. The strict phylogeographic pattern suggests that the present population generic structure in field voles reflects glacial history: the two groups are derived from different glacial refugia, and recolonized Fennoscandia from two directions. A 150–200-km-wide secondary contact zone between the two mtDNA groups was found in northern Sweden. Distinct phylogeographic substructuring was observed within both major mtDNA groups.     

Phylogeography of the California sheephead,Semicossyphus pulcher: the role of deep reefs as stepping stones and pathways to antitropicality

In the past decade, the study of dispersal of marine organisms has shifted from focusing predominantly on the larval stage to a recent interest in adult movement. Antitropical distributions provide a unique system to assess vagility and dispersal. In this study, we have focused on an antitropical wrasse genus, Semicossyphus, which includes the California sheephead, S. pulcher, and Darwin's sheephead, S. darwini. Using a phylogenetic approach based on mitochondrial and nuclear markers, and a population genetic approach based on mitochondrial control region sequences and 10 microsatellite loci, we compared the phylogenetic relationships of these two species, as well as the population genetic characteristics within S. pulcher. While S. pulcher and S. darwini are found in the temperate eastern Pacific regions of the northern and southern hemispheres, respectively, their genetic divergence was very small (estimated to have occurred between 200 and 600 kya). Within S. pulcher, genetic structuring was generally weak, especially along mainland California, but showed weak differentiation between Sea of Cortez and California, and between mainland California and Channel Islands. We highlight the congruence of weak genetic differentiation both within and between species and discuss possible causes for maintenance of high gene flow. In particular, we argue that deep and cooler water refugia are used as stepping stones to connect distant populations, resulting in low levels of genetic differentiation.     

Intraspecific Phylogeography of Red Squirrels (Tamiasciurus hudsonicus) in the Central Rocky Mountain Region of North America

We used variation in a portion of the mitochondrial DNA control region to examine phylogeography of Tamiasciurus hudsonicus, a boreal-adapted small mammal in the central Rocky Mountain region. AMOVA revealed that 65.66% of genetic diversity was attributable to variation within populations, 16.93% to variation among populations on different mountain ranges, and 17.41% to variation among populations within mountain ranges. Nested clade analysis revealed two major clades that likely diverged in allopatry during the Pleistocene: a southern clade from southern Colorado and a northern clade comprising northern Colorado, Wyoming, eastern Utah, and eastern Idaho. Historically restricted gene flow as a result of geographic barriers was indicated between populations on opposite sides of the Green River and Wyoming Basin and among populations in eastern Wyoming. In some instances genetic structure indicated isolation by distance.     

Intraspecific molecular phylogeny and phylogeography of the Meriones meridianus (Rodentia: Cricetidae) complex in northern China reflect the processes of desertification and the Tianshan Mountains uplift

The phylogeographical patterns and demographic history of mitochondrial DNA (cytochrome b, N = 327; D‐loop, N = 252) and nuclear DNA (IRBP gene, N = 235) haplotypes were studied for the Meriones meridianus complex in northern China, a desert‐dwelling gerbil species complex. The phylogenetic analyses, which were performed on the separate and combined (mitochondrial + nuclear) datasets, revealed two divergent clades (Clade A and Clade B) corresponding to distinct geographical regions. Clade A contained the haplotypes found mostly in individuals from the Tianshan Mountains area. Clade B contained haplotypes from populations located in other deserts in northern China. The divergence times indicated that the history of the M. meridianus complex was influenced by the uplift of the Tianshan Mountains and climate‐induced habitat fluctuations. In the Pleistocene, the expansion of forests and grasslands during interglacial period led to the isolation of the M. meridianus complex, which preferred to inhabit deserts. Hence, long geological isolation and the M. meridianus complex adaptation to local ecological conditions led to its genetic divergence. Clade A had long‐lasting demographic stability, most likely because the populations of this clade remained in a stable desert environment for a long time. However, the extension of other deserts and disappearance of palaeolakes during the last glacial period resulted in demographic expansion of Clade B. Furthermore, our genetic data indicated that two subspecies may exist within the M. meridianus complex. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 362–383.     

Population structure of the Indonesian giant tiger shrimp Penaeus monodon: a window into evolutionary similarities between paralogous mitochondrial DNA sequences and their genomes

Here we used both microsatellites and mtCR (mitochondrial DNA control region) sequences as genetic markers to examine the genetic diversity and population structure of Penaeus monodon shrimp from six Indonesian regions. The microsatellite data showed that shrimp from the Indian and the Pacific Ocean were genetically distinct from each other. It has been reported previously that P. monodon mtCR sequences from the Indo‐Pacific group into two major paralogous clades of unclear origin. Here we show that the population structure inferred from mtCR sequences matches the microsatellite‐based population structure for one of these clades. This is consistent with the notion that this mtCR clade shares evolutionary history with nuclear DNA and may thus represent nuclear mitochondrial pseudogenes (Numts).     

Cranial morphology of the California vole (Microtus californicus,Cricetidae) in a contact zone

Zones of contact between divergent biological forms within or between species are critical to the study of speciation. How characters flow across contact zones can be informative of the speciation process. To better understand this phenomenon in a mammal, we investigated cranial shape change in a contact zone between northern and southern phylogeographical groups of California voles (Microtus californicus). We took 12 linear measurements of skulls, one measurement of the mandible, and coded the presence and absence of two skull foramina for 427 specimens. In multivariate analyses, skulls within parental regions were correctly assigned more than 90% of the time. In the contact zone, 49% were classified as northern and 51% as southern, with a bimodal distribution of posterior probability values. Foraminal patterns in the contact zone were intermediate between northern and southern regions. A cline analysis for coastal populations suggested a similar centre for mitochondrial and nuclear markers, although a centre for the morphological data was offset. Cranial morphology indicates an intermediate area with overlap between the two regions, as suggested by the molecular data, with a pattern distinct from mitochondrial DNA or nuclear DNA markers. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 264–283.     

Genetic structure of desert ground squirrels over a 20-degree-latitude transect from Oregon through the Baja California peninsula

The genetic structure of populations over a wide geographical area should reflect the demographic and evolutionary processes that have shaped a species across its range. We examined the population genetic structure of antelope ground squirrels (Ammospermophilus leucurus) across the complex of North American deserts from the Great Basin of Oregon to the cape region of the Baja California peninsula. We sampled 73 individuals from 13 major localities over this 2500-km transect, from 43 to 22 degrees north. Our molecular phylogeographical analysis of 555 bp of the mitochondrial cytochrome b gene and 510 bp of the control region revealed great genetic uniformity in a single clade that extends from Oregon to central Baja California. A second distinct clade occupies the southern half of the peninsula. The minimal geographical structure of the northern clade, its low haplotype diversity and the distribution of pairwise differences between haplotypes suggest a rapid northward expansion of the population that must have followed a northward desert habitat shift associated with the most recent Quaternary climate warming and glacial retreat. The higher haplotype diversity within the southern clade and distribution of pairwise differences between haplotypes suggest that the southern clade has a longer, more stable history associated with a southern peninsular refugium. This system, as observed, reflects both historical and contemporary ecological and evolutionary responses to physical environmental gradients within genetically homogeneous populations.     

Phylogeography and Pleistocene refugia of the Little Owl Athene noctua inferred from mtDNA sequence data

Pleistocene glaciations greatly affected the distribution of genetic diversity in animal populations. The Little Owl is widely distributed in temperate regions and could have survived the last glaciations in southern refugia. To describe the phylogeographical structure of European populations, we sequenced the mitochondrial cytochrome c oxidase I (COI) and control region (CR1) in 326 individuals sampled from 22 locations. Phylogenetic analyses of COI identified two deeply divergent clades: a western haplogroup distributed in western and northwestern Europe, and an eastern haplogroup distributed in southeastern Europe. Faster evolving CR1 sequences supported the divergence between these two main clades, and identified three subgroups within the eastern clade: Balkan, southern Italian and Sardinian. Divergence times estimated from COI with fossil calibrations indicate that the western and eastern haplogroups split 2.01–1.71 Mya. Slightly different times for splits were found using the standard 2% rate and 7.3% mtDNA neutral substitution rate. CR1 sequences dated the origin of endemic Sardinian haplotypes at 1.04–0.26 Mya and the split between southern Italian and Balkan haplogroups at 0.72–0.21 Mya, coincident with the onset of two Pleistocene glaciations. Admixture of mtDNA haplotypes was detected in northern Italy and in central Europe. These findings support a model of southern Mediterranean and Balkan refugia, with postglacial expansion and secondary contacts for Little Owl populations. Central and northern Europe was predominantly recolonized by Little Owls from Iberia, whereas expansion out of the Balkans was more limited. Northward expansion of the Italian haplogroup was probably prevented by the Alps, and the Sardinian haplotypes remained confined to the island. Results showed a clear genetic pattern differentiating putative subspecies. Genetic distances between haplogroups were comparable with those recorded between different avian species.     

Extensive genetic differentiation in Gobiomorphus breviceps from New Zealand

Partial mitochondrial DNA sequences for parts of the cytochrome b gene and control region were obtained for 89 upland bullies Gobiomorphus breviceps from 19 catchments in New Zealand. There were two highly distinctive mtDNA clades: a northern clade corresponding to the North Island, northern South Island and west coast South Island, and a south‐east clade, in the southern and eastern South Island. Within these major clades there were further distinct clades that correlated with geographic sub‐regions and catchments. The marked genetic differentiation has occurred in the absence of obvious morphological divergence. Based on cytochrome b sequence divergences and the molecular clock hypothesis, the northern and southeastern clades correspond with the uplift of the Southern Alps during the Pliocene, while populations in the North Island and northern South Island were estimated to have diverged during the Pleistocene. The widescale geographic divergences were similar to those observed in the galaxiids, Galaxias vulgaris and Galaxias divergens , but biogeographic management boundaries may not be the same, reflecting different evolutionary histories for non‐diadromous species occupying the same areas.     

Phylogeography of the Trans‐Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south‐eastern Mexico

We quantify the population divergence processes that shaped population genetic structure in the Trans‐Volcanic bunchgrass lizard (Sceloporus bicanthalis) across the highlands of south‐eastern Mexico. Multilocus genetic data from nine nuclear loci and mitochondrial (mt)DNA were used to estimate the population divergence history for 47 samples of S. bicanthalis. Bayesian clustering methods partitioned S. bicanthalis into three populations: (1) a southern population in Oaxaca and southern Puebla; (2) a population in western Puebla; and (3) a northern population with a broad distribution across Hidalgo, Puebla, and Veracruz. The multilocus nuclear data and mtDNA both supported a Late Pleistocene increase in effective population size, and the nuclear data revealed low levels of unidirectional gene flow from the widespread northern population into the southern and western populations. Populations of S. bicanthalis experienced different demographic histories during the Pleistocene, and phylogeographical patterns were similar to those observed in many co‐distributed highland taxa. Although we recommend continuing to recognize S. bicanthalis as a single species, future research on the evolution of viviparity could gain novel insights by contrasting physiological and genomic patterns among the different populations located across the highlands of south‐eastern Mexico. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 852–865.     

Pleistocene refugia in an arid landscape: analysis of a widely distributed Australian passerine

While many studies have documented the effect that glacial cycles have had on northern hemisphere species, few have attempted to study the associated effect of aridification at low latitudes in the southern hemisphere. We investigated the past effects that cyclic aridification may have had on the population structure and history of a widespread endemic Australian bird species, the Australian magpie (Gymnorhina tibicen). One thousand one hundred and sixty-six samples from across its native range were analysed for mitochondrial control region sequence variation and variation at six microsatellite loci. Analysis of mitochondrial control region sequence data indicated monophyletic clades that were geographically congruent with an eastern and western region. The contemporary distribution of east and west clades is nonoverlapping but in close proximity. Populations were estimated to have diverged in the Pleistocene around 36,000 years ago. The putative Carpentarian and Nullarbor arid barriers appear to be associated with the divergence between east and west mainland populations. Nested clade analysis indicated a signature of range expansion in the eastern region suggesting movement possibly inland and northward subsequent to the last period of aridity. The island population of Tasmania was of very recent origin, possibly since sea levels rose 16,000 years ago. Given the east-west structure, there was no congruence between morphology and recent history of this species indicating a lack of support for morphological taxa. Overall mitochondrial DNA and microsatellite variation suggest that increasing aridity and Pleistocene refugia played a role in structuring populations of the Australian magpie; however, the dispersal ability and generalist habitat requirements may have facilitated the movement of magpies into an almost contiguous modern distribution across the continent. This study supports the idea that Pleistocene aridification played an important role in structuring intraspecific variation in low latitudinal southern hemisphere avian species.     

Genetic differentiation and inferred dynamics of a hybrid zone between Northern Spotted Owls (Strix occidentalis caurina) and California Spotted Owls (S. o. occidentalis) in northern California

Genetic differentiation among Spotted Owl (Strix occidentalis) subspecies has been established in prior studies. These investigations also provided evidence for introgression and hybridization among taxa but were limited by a lack of samples from geographic regions where subspecies came into close contact. We analyzed new sets of samples from Northern Spotted Owls (NSO: S. o. caurina) and California Spotted Owls (CSO: S. o. occidentalis) in northern California using mitochondrial DNA sequences (mtDNA) and 10 nuclear microsatellite loci to obtain a clearer depiction of genetic differentiation and hybridization in the region. Our analyses revealed that a NSO population close to the northern edge of the CSO range in northern California (the NSO Contact Zone population) is highly differentiated relative to other NSO populations throughout the remainder of their range. Phylogenetic analyses identified a unique lineage of mtDNA in the NSO Contact Zone, and Bayesian clustering analyses of the microsatellite data identified the Contact Zone as a third distinct population that is differentiated from CSO and NSO found in the remainder of the subspecies' range. Hybridization between NSO and CSO was readily detected in the NSO Contact Zone, with over 50% of individuals showing evidence of hybrid ancestry. Hybridization was also identified among 14% of CSO samples, which were dispersed across the subspecies' range in the Sierra Nevada Mountains. The asymmetry of hybridization suggested that the hybrid zone may be dynamic and moving. Although evidence of hybridization existed, we identified no F1 generation hybrid individuals. We instead found evidence for F2 or backcrossed individuals among our samples. The absence of F1 hybrids may indicate that (1) our 10 microsatellites were unable to distinguish hybrid types, (2) primary interactions between subspecies are occurring elsewhere on the landscape, or (3) dispersal between the subspecies' ranges is reduced relative to historical levels, potentially as a consequence of recent regional fires.