Mitochondrial genome recombination in the zone of contact between two hybridizing conifers

Variation in mitochondrial DNA was surveyed at four gene loci in and around the zone of contact between two naturally hybridizing conifers, black spruce (Picea mariana) and red spruce (P. rubens) in northeastern North America. Most of the mtDNA diversity of these species was found in populations next to or into the zone of contact, where some individuals bore rare mitotypes intermediate between the common mitotypes observed in the allopatric areas of each species. Sequence analysis and tests for mtDNA recombination point to this phenomenon, rather than to recurrent mutation, as the most tenable hypothesis for the origin of these rare mitotypes. From the 10 mitotypes observed, at least 4 would be the product of recombination between 4 of the 5 putative ancestral mitotypes. Tests for cytonuclear disequilibrium and geographical structure of the putative recombinant mitotypes suggest that mtDNA recombination is not frequent and relatively recent on the geological time scale. mtDNA recombination would have been promoted by transient heteroplasmy due to leakage of paternal mtDNA since the Holocene secondary contact between the two species.     

New evidence from mitochondrial DNA of a progenitor-derivative species relationship between black spruce and red spruce (Pinaceae)

Mitochondrial DNA (mtDNA) markers were used to assess the genetic diversity in allopatric populations of black spruce (Picea mariana [Mill.] BSP) and red spruce (P. rubens Sarg.). Patterns of mitochondrial haplotypes (mitotypes) were strikingly different between the two species. All mtDNA markers surveyed were polymorphic in black spruce, revealing four different mitotypes and high levels of mtDNA diversity (P(p) = 100%, A = 2.0, H = 0.496). In contrast, populations of red spruce had only two mitotypes and harbored low levels of ggenetic diversity (P(p) = 13.2%, A = 1.1, H = 0.120). When the southernmost allopatric populations of red spruce were considered, only one mitotype was detected. As previously reported for nuclear gene loci, the diversity observed for mtDNA in red spruce was a subset of that found in black spruce. Comparison of present and previously published data supports the hypothesis of a recent progenitor-derivative relationship between these species, red spruce presumably being derived by allopatric speciation of an isolated population of black spruce during the Pleistocene.     

Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan

The phylogegraphic pattern of Cycas taitungensis, an endemic species with two remaining populations in Taiwan, was investigated based on genetic variability and phylogeny of the atpB-rbcL noncoding spacer of chloroplast DNA (cpDNA) and the ribosomal DNA (rDNA) internal transcribed spacer (ITS) of mitochondrial DNA (mtDNA). High levels of genetic variation at both organelle loci, due to frequent intramolecular recombination, and low levels of genetic differentiation were detected in the relict gymnosperm. The apportionment of genetic variation within and between populations agreed with a migrant-pool model, which describes a migratory pattern with colonists recruited from a random sample of earlier existing populations. Phylogenies obtained from cpDNA and mtDNA were discordant according to neighbour-joining analyses. In total four chlorotypes (clades I-IV) and five mitotypes (clades A-E) were identified based on minimum spanning networks of each locus. Significant linkage disequilibrium in mitotype-chlorotype associations excluded the possibility of the recurrent homoplasious mutations as the major force causing phylogenetic inconsistency. The most abundant chlorotype I was associated with all mitotypes and the most abundant mitotype C with all chlorotypes; no combinations of rare mitotypes with rare chlorotypes were found. According to nested clade analyses, such nonrandom associations may be ascribed to relative ages among alleles associated with the geological history through which cycads evolved. Nested in networks as interior nodes coupled with wide geographical distribution, the most dominant cytotypes of CI and EI may represent ancestral haplotypes of C. taitungensis with a possible long existence prior to the Pleistocene glacial maximum. In contrast, rare chlorotypes and mitotypes with restricted and patchy distribution may have relatively recent origins. Newly evolved genetic elements of mtDNA, with a low frequency, were likely to be associated with the dominant chlorotype, and vice versa, resulting in the nonrandom mitotype-chlorotype associations. Paraphyly of CI and EI cytotypes, leading to the low level of genetic differentiation between cycad populations, indicated a short period for isolation, which allowed low possibilities of the attainment of coalescence at polymorphic ancestral alleles.     

Comparative genetic stock structure in three species of commercially exploited Indo-Malay Carangidae (Teleosteii,Perciformes)

We examine genetic structuring in three commercially important species of the teleost family Carangidae from Malaysian waters: yellowtail scad Atule mate, bigeye scad Selar crumenophthalmus and yellowstripe scad Selaroides leptolepis, from the Indo-Malay Archipelago. In view of their distribution across contrasting habitats, we tested the hypothesis that pelagic species display less genetic divergence compared with demersal species, due to their potential to undertake long-distance migrations in oceanic waters. To evaluate population genetic structure, we sequenced two mitochondrial (mt)DNA [650 bp of cytochrome oxidase I (coI), 450 bp of control region (CR)] and one nuclear gene (910 bp of rag1) in each species. One hundred and eighty samples from four geographical regions within the Indo-Malay Archipelago including a population of yellowtail from Kuwait were examined. Findings revealed that the extent of genetic structuring among populations in the semi-pelagic and pelagic, yellowtail and bigeye were lower than demersal yellowstripe, consistent with the hypothesis that pelagic species display less genetic divergence compared with demersal species. The yellowtail phylogeny identified three distinct clades with bootstrap values of 86%–99% in mtDNA and 63%–67% in rag1. However, in bigeye, three clades were also observed from mtDNA data while only one clade was identified in rag1 dataset. In yellowstripe, the mtDNA tree was split into three closely related clades and two clades in rag1 tree with bootstraps value of 73%–99% and 56% respectively. However, no geographic structure appears in both mtDNA and rag1 datasets. Hierarchical molecular variance analysis (AMOVA), pair wise F_ST comparisons and the nearest-neighbour statistic (S_nn) showed significant genetic differences among Kuwait and Indo-Malay yellowtail. Within the Indo-Malay Archipelago itself, two distinct mitochondrial lineages were detected in yellowtail suggesting potential cryptic species. Findings suggests varying degrees of genetic structuring, key information relevant to management of exploited stocks, though more rapidly evolving genetic markers should be used in future to better delimit the nature and dynamics of putative stock boundaries.     

Variation in mitochondrial DNA reveals multiple distant glacial refugia in black spruce (Picea mariana), a transcontinental North American conifer

Range-wide genetic variation of black spruce (Picea mariana) was studied using polymerase chain reaction-random fragment length polymorphism markers of the mitochondrial genome. Four polymorphic mitochondrial DNA (mtDNA) loci were surveyed and two or three alleles were detected at each locus, resulting in 10 multilocus mtDNA types or mitotypes. A significant subdivision of population genetic diversity was detected (GST = 0.671; NST = 0.726), suggesting low levels of gene flow among populations. The distribution of mitotypes was not random (NST > GST; P < 0.05) and revealed four partially overlapping zones, presumably representative of different glacial populations. Comparison of the genetic structure derived from mtDNA markers and the colonization paths previously deduced from the fossil and pollen records allow us to infer at least three southern and one northeastern glacial populations for black spruce. The patterns revealed in this study suggest that black spruce shares its biogeographical history with other forest-associated North American species.     

Contrasting phylogeographical patterns between mainland and island taxa of the Pinus luchuensis complex

Species whose geographical distribution encompasses both mainland and island populations provide an ideal system for examining isolation and genetic divergence. In this study, paternally transmitted chloroplast DNA (cpDNA) and maternally transmitted mitochondrial DNA (mtDNA) were used to estimate population structure and phylogeography of Pinus luchuensis, a species found in eastern China (ssp. hwangshanensis), Taiwan (ssp. taiwanensis), and the Ryukyu Archipelago (ssp. luchuensis). Gene genealogies of both mtDNA and cpDNA reveal two major lineages. Molecular dating indicates that these lineages diverged before the colonization of P. luchuensis subspecies in Taiwan and the Ryukyu Archipelago. Both mtDNA and cpDNA show a lack of correspondence between molecular phylogeny and subspecies designation. Phylogeographical analysis suggests that paraphyly of the subspecies is the result of recent divergence rather than secondary contacts. In spite of the short divergence history of P. luchuensis on islands, the island populations show the same degree of genetic divergence as mainland populations. Low levels of genetic diversity in the mainland ssp. hwangshanensis suggest demographic bottlenecks. In contrast, the high heterogeneity of genetic composition for island populations is likely to be associated with a history of multiple colonization from the mainland. The spatial apportionment of organelle DNA polymorphisms is consistent with a pattern of stepwise colonization on island populations.     

The incomplete history of mitochondrial lineages between two rockfishes, Sebastes longispinis and Sebastes hubbsi (Scorpaeniformes: Scorpaenidae)

The genetic divergence between two closely related rockfishes, Sebastes longispinis and Sebastes hubbsi, was inferred from both mitochondrial DNA (mtDNA) sequence variations and amplified fragment length polymorphism (AFLP) markers. The two species were placed into two distinct clades in a neighbour-joining tree based on the AFLP data, clearly indicating that they represented separate species. Although this evidence, together with a previous morphological study, revealed clear differences between the two species, no obvious clustering of haplotypes by species was detected in the minimum spanning network inferred from sequence variations in the mtDNA control region (c. 500 base pairs). In fact, the significant Φ(ST) estimates indicated only a restriction of gene flow between the two species. Uncorrected pairwise sequence differences in mtDNA between two species were small (1·8% at maximum, on the lower end of the range of control region divergence between previously studied sister species pairs), suggesting their speciation event as having been fairly recent. The incongruent results of AFLP and mtDNA phylogenies suggested incomplete lineage sorting and introgression of mtDNA in the course of the evolution of the two species. Differences in their main distributional ranges and the small level of sequence divergence in mtDNA suggests that speciation and dispersal may have been associated with glacio-eustatic sea level fluctuations between the Japanese Archipelago and the Korean Peninsula during the past 0·4 million years.     

Inferences from mitochondrial DNA patterns on the domestication history of alfalfa (Medicago sativa)

The evolutionary history of a wild-cultivated complex is the outcome of different factors, among which are the domestication of the cultivated form, its geographical and demographic expansion, as well as gene flow between natural and cultivated populations. To clarify this history for alfalfa (Medicago sativa), we adopted a phylogeographical approach based on a sample of natural and cultivated populations of the M. sativa species complex. This sample was characterized for mtDNA variation through restriction fragment length polymorphisms. Twenty-two mitotypes were identified in the whole data set (155 individuals). In the wild pool from the presumed area of origin (Near East to Central Asia), the diversity was high but the absence of geographical differentiation hinders a more precise location of the centre of domestication. Within the cultivated alfalfa, the geographical structure suggests strongly the existence of at least two independent routes of dissemination of alfalfa from its centre of origin. In particular, original mitotypes detected in some regions suggest that wild populations not sampled in this study, and located outside the presumed area of domestication, may have contributed to the diversity of the cultivated pool. Finally, analysis of the mtDNA variation shows that natural populations collected in Spain constitute an endemic wild pool now introgressed partially by cultivated alfalfa.     

Individual performance in relation to cytonuclear discordance in a northern contact zone between long‐toed salamander (Ambystoma macrodactylum) lineages

Cytonuclear discordance in contact zones between related lineages is common, with mitochondrial clines often being displaced from clines in nuclear allele frequency. Proposed explanations for such a pattern include adaptive introgression of mtDNA or a neutral wake of mtDNA being left behind following hybrid zone movement. However, studies investigating these hypotheses are rare. Our previous survey of genetic variation in the long‐toed salamander (Ambystoma macrodactylum) highlighted a potential case of cytonuclear discordance between two lineages in western Canada. Here, we use additional markers and samples to clarify the extent of this discordance. We simultaneously assess the feeding performance of individuals in a common environment to test for an association between mitotype and individual performance. The genetic results confirm a general pattern of cytonuclear discordance in the focal region. However, we also observed more limited introgression of a diagnostic nuclear marker. Intriguingly, although there were differences in individual performance associated with the transition between mitotypes, these differences were not fully explained by mitotype. Instead, the lowest performance was observed in individuals demonstrating the greatest mismatch between mtDNA and all nuclear markers, suggesting the potential for cytonuclear incompatibilities to be acting. These results highlight the complexity of understanding the causes and consequences of mtDNA introgression and cytonuclear discordance in contact zones.     

Evidence of doubly uniparental inheritance of the mitochondrial DNA in Polititapes rhomboides (Bivalvia,Veneridae): Evolutionary and population genetic analysis of F and M mitotypes

Doubly uniparental inheritance (DUI) is a particular mitochondrial DNA inheritance mode reported in a number of bivalves. DUI species show two types of mtDNA, one transmitted from females to daughters and sons (F mitotype) and another one from males to sons (M mitotype). In Veneridae, the existence of DUI has been investigated in several species but it was found in only two of them. In this study, we obtained partial sequences of rrnL, cytb and cox1 genes of males and females of Polititapes rhomboides from NW Spain and we demonstrated the existence of heteroplasmy in males, as expected under DUI. F and M mitotypes showed a taxon-specific phylogenetic pattern and similar evolutionary rates. We focused on cox1 for population genetic analysis, examining separately F and M mitotypes, but also F mitotypes from females (F_♀) and males (F_♂). In all cases, cox1 bears signs of strong purifying selection, with no apparent evidence of relaxed selection in the M genome, while the divergence between F and M genomes is in agreement with the neutral model of evolution. The cox1 polymorphism, higher at the M than at the F genome, also shows clear footprints of genetic hitchhiking with favourable mutations at other mtDNA loci, except for F_♂. In terms of population structure, results suggest that the pattern depends on the examined mitotype (F, F_♀, F_♂ or M).     

Comparative phylogeography of two bitterlings, Tanakia lanceolata and T. limbata (Teleostei, Cyprinidae), in Kyushu and adjacent districts of western Japan, based on mitochondrial DNA analysis

To understand the geographical patterns of genetic variation in freshwater fishes in western Japan, the genetic structures of populations of Tanakia lanceolata and T. limbata (Teleostei, Cyprinidae) in this area were investigated using mitochondrial DNA (mtDNA) cytb sequences. Neighbor-joining trees of mtDNA haplotypes revealed four and three genetically divergent groups in T. lanceolata and T. limbata, respectively. Each group was restricted to one or the other of the geographical regions in the area studied. The patterns of geographical divergence in the two species showed some similarities, which seem to reflect common historical events experienced by freshwater fishes distributed in western Japan. On the other hand, dissimilarities were also found in the patterns, indicating that species-specific historical processes also occurred. Within one region, T. lanceolata was less differentiated than T. limbata, suggesting a difference in the dispersal abilities of the two bitterlings. In addition, several individuals in Kunichika River on Shikoku island were morphologically identified as T. lanceolata but had mtDNA haplotypes of T. limbata. We tentatively suggest that these individuals are hybrids of the two species, but further studies employing nuclear markers are necessary to validate this hypothesis.     

Decoupled mitochondrial and chloroplast DNA population structure reveals Holocene collapse and population isolation in a threatened Mexican-endemic conifer

Chihuahua spruce (Picea chihuahuana Martínez) is a montane subtropical conifer endemic to the Sierra Madre Occidental in northwestern México. Range-wide variation was investigated using maternally inherited mitochondrial (mtDNA) and paternally inherited chloroplast (cpDNA) DNA markers. Among the 16 mtDNA regions analysed, only two mitotypes were detected, while the study of six cpDNA microsatellite markers revealed eight different chlorotypes. The average cpDNA diversity (H = 0.415) was low but much higher than that for mtDNA (H = 0). The distribution of mitotypes revealed two clear nonoverlapping areas (G(ST) = N(ST) = 1), one including northern populations and the second one including the southern and central stands, suggesting that these two regions may represent different ancestral populations. The cpDNA markers showed lower population differentiation (G(ST) = 0.362; R(ST) = 0.230), implying that the two ancestral populations continued to exchange pollen after their initial geographic separation. A lack of a phylogeographic structure was revealed by different spatial analyses of cpDNA (G(ST) > R(ST); and samova), and reduced cpDNA gene flow was noted among populations (Nm = 0.873). Some stands deviated significantly from the mutation-drift equilibrium, suggesting recent bottlenecks. Altogether, these various trends are consistent with the hypothesis of a population collapse during the Holocene warming and suggest that most of the modern P. chihuahuana populations are now effectively isolated with their genetic diversity essentially modelled by genetic drift. The conservation efforts should focus on most southern populations and on the northern and central stands exhibiting high levels of genetic diversity. Additional mtDNA sequence analysis confirmed that P. martinezii (Patterson) is not conspecific with P. chihuahuana, and thus deserves separate conservation efforts.     

MULTIPLE ORIGINS OF GENDER-ASSOCIATED MITOCHONDRIAL DNA LINEAGES IN BIVALVES (MOLLUSCA: BIVALVIA)

Previous studies have shown that marine mussels (genus Mytilus) and a freshwater mussel (Pyganodon grandis) contain two distinct gender-associated mitotypes, which is a characteristic feature of the phenomenon of doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA). Here we present evidence for the presence of distinct male (M) and female (F) mitotypes in three other bivalve species, the mytilid Geukensia demissa, and the unionid species P. fragilis and Fusconaia flava. Nucleotide sequences of a segment of the COI gene from the M and F mitotypes from each of the three mytilid species (M. edulis, M. trossulus, G. demissa) and three unionid species (P. grandis, P. fragilis, F. flava) were used for phylogenetic analysis. The analysis suggests three independent origins of M and F mitotypes for the six species examined; one for the three unionid species, one for the two Mytilus species, and one for Geukensia. The first of these F/M divergence events, while of uncertain age, predates the divergence of the two unionid genera and is likely older than either of the two F/M divergence events in the mytilid taxa. The most parsimonious explanation of multiple F/M divergence events is that they represent independent origins of DUI. Another possibility is that, in a given taxon, an F or M mitotype assumes the role of the opposite mitotype (by virtue of a mechanism that remains to be clarified) and subsequently was fixed within its new gender. The fixation of a mtDNA lineage derived from a mitotype of switched function would reset the divergence of the gender-associated lineages to zero, thereby mimicking a de novo split of F and M lineages from a preexisting mtDNA genome that was not gender specific. Further broad-scale taxonomic studies of the occurrence of distinct M and F mitotypes may allow for the evaluation of the latter hypothesis.     

Phylogeography of the Japanese pipistrelle bat,Pipistrellus abramus,in China: the impact of ancient and recent events on population genetic structure

The influence of Pleistocene climatic oscillations on shaping the genetic structure of Asian biota is poorly known. The Japanese pipistrelle bat occurs over a wide range in eastern Asia, from Siberia to Japan. To test the relative impact of ancient and more recent events on genetic structure in this species, we combined mitochondrial (cytochrome b) and microsatellite markers to reconstruct its phylogeographic and demographic history on continental China and its offshore islands, Hainan Island and the Zhoushan Archipelago. Our mitochondrial DNA tree recovered two divergent geographical clades, indicating multiple glacial refugia in the region. The first clade was mainly confined to Hainan Island, indicating that gene flow between this population and the continent has been restricted, despite being repeatedly connected to the mainland during repeated glacial episodes. By contrast, haplotypes sampled on the Zhoushan Archipelago were mixed with those from the mainland, suggesting a recent shared history of expansion. Although microsatellite allele frequencies showed clear discontinuities across the sampling range, supporting the current isolation of both Hainan Island and the Zhoushan Archipelago, we also found clear evidence of more recent back colonization, probably via post‐glacial expansion or, in the latter case, occasional long distance dispersal. The results obtained highlight the importance of using multiple sets of markers for teasing apart the roles of ancient and more recent events on population genetic structure. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 582–594.     

Phylogeography of Eastern Polynesian sandalwood (Santalum insulare), an endangered tree species from the Pacific: a study based on chloroplast microsatellites

Aim Patterns of genetic variation within forest species are poorly documented in island ecosystems. The distribution of molecular variation for Santalum insulare, an endangered tree species endemic to the islands of eastern Polynesia, was analysed using chloroplast microsatellite markers. The aims were to quantify the genetic diversity; to assess the genetic structure; and to analyse the geographical distribution of the diversity within and between archipelagoes. The ultimate goal was to pre‐define evolutionary significant units (ESUs) for conservation and restoration programmes of this species, which constitutes a natural resource on small, isolated islands. Location Eleven populations, each representative of one island, covering most of the natural occurrence of S. insulare were sampled: five populations from the Marquesas Archipelago; three from the Society Archipelago; and three from the Cook–Austral Archipelago. These South Pacific islands are known for their high degree of plant endemism, and for their human occupation by Polynesian migrations. The extensive exploitation of sandalwood by Europeans nearly 200 years ago for its fragrant heartwood, used overseas in incense, carving and essential oil production for perfume, has dramatically reduced the population size of this species. Methods We used chloroplast microsatellites, which provide useful information in phylogeographical forest tree analyses. They are maternally inherited in most angiosperms and present high polymorphism. Among the 499 individuals sampled, 345 were genotyped successfully. Classical models of population genetics were used to assess diversity parameters and phylogenetic relationships between populations. Results Four microsatellite primers showed 16 alleles and their combinations provided 17 chlorotypes, of which four exhibited a frequency > 10% in the total population. The gene diversity index was high for the total population (H_e = 0.82) and varied among archipelagoes from H_e = 0.40 to 0.67. Genetic structure is characterized by high levels of differentiation between archipelagoes (36% of total variation) and between islands, but differentiation between islands varied according to archipelago. The relationship between genetic and geographical distance confirms the low gene flow between archipelagoes. The minimum spanning tree of chlorotypes exhibits three clusters corresponding to the geographical distribution in the three main archipelagoes. Main conclusions The high level of diversity within the species was explained by an ancient presence on and around the hotspot traces currently occupied by young islands. Diversity in the species has enabled survival in a range of habitats. Relationships between islands show that the Cook–Austral chlorotype cluster constitutes a link between the Marquesas and the Society Islands. This can be explained by the evolution of the island systems over millions of years, and extinction of intermediary populations on the Tuamotu Islands following subsidence there. Based on the unrooted neighbour‐joining tree and on the genetic structure, we propose four ESUs to guide the conservation and population restoration of Polynesian Sandalwood: the Society Archipelago; the Marquesas Archipelago; Raivavae Island; and Rapa Island.     

Phylogeography of the endangered Cathaya argyrophylla (Pinaceae) inferred from sequence variation of mitochondrial and nuclear DNA

Cathaya argyrophylla is an endangered conifer restricted to subtropical mountains of China. To study phylogeographical pattern and demographic history of C. argyrophylla, species-wide genetic variation was investigated using sequences of maternally inherited mtDNA and biparentally inherited nuclear DNA. Of 15 populations sampled from all four distinct regions, only three mitotypes were detected at two loci, without single region having a mixed composition (G(ST) = 1). Average nucleotide diversity (theta(ws) = 0.0024; pi(s) = 0.0029) across eight nuclear loci is significantly lower than those found for other conifers (theta(ws) = 0.003 approximately 0.015; pi(s) = 0.002 approximately 0.012) based on estimates of multiple loci. Because of its highest diversity among the eight nuclear loci and evolving neutrally, one locus (2009) was further used for phylogeographical studies and eight haplotypes resulting from 12 polymorphic sites were obtained from 98 individuals. All the four distinct regions had at least four haplotypes, with the Dalou region (DL) having the highest diversity and the Bamian region (BM) the lowest, paralleling the result of the eight nuclear loci. An AMOVA revealed significant proportion of diversity attributable to differences among regions (13.4%) and among populations within regions (8.9%). F(ST) analysis also indicated significantly high differentiation among populations (F(ST) = 0.22) and between regions (F(ST) = 0.12-0.38). Non-overlapping distribution of mitotypes and high genetic differentiation among the distinct geographical groups suggest the existence of at least four separate glacial refugia. Based on network and mismatch distribution analyses, we do not find evidence of long distance dispersal and population expansion in C. argyrophylla. Ex situ conservation and artificial crossing are recommended for the management of this endangered species.     

Genetic differentiation of the inhabitants of Mongolia. Geographic distribution of mitochondrial DNA RFLPs and mitotypes in the inhabitants of Mongolia and a population assessment of the mutation rate in the mitochondrial genome]

The geographical distribution of the Asian specific deletion--insertion polymorphisms and or the RFLP's in the V noncoding region and the D-loop and of the mitotypes was analysed in Mongolia. The frequencies of the mtDNA markers demonstrated homogeneity of 18 local groups in Mongolia. The geographical distribution of the mitotypes showed the existence of two ancestral maternal lineages in mongols. There was no significant difference in the average FST values between mitochondrial gene flow and the nuclear gene flow of the Mongolian population. The equality of FST values permit to calculate the mutation rate for the human mtDNA--6.10(-9) per nucleotide per year. The data reveals the Mongolian population is in the equilibrium.     

Study of hybridization in four species of ground squirrels (spermophilus: Rodentia,Sciuridae) by molecular genetic methods

Four species of ground squirrel--yellow (Spermophilus fulvus), russet (S. major), small (S. pygmaeus), and spotted (S. suslicus)--occur in the Volga region. Between S. major and S. pigmaeus, S. major and S. fulvus, and S. major and S. suslicus, sporadic hybridization was reported. Using sequencing and restriction analysis, we have examined the mtDNA C region in 13 yellow, 60 russet, 61 small, 45 spotted ground squirrels, and 9 phenotypic hybrids between these species. It was shown that 43% of S. major individuals had "alien" mitotypes typical of S. fulvus and S. pygmaeus. Alien mitotypes occurred both within and outside sympatric zones. No alien mitotypes were found in 119 animals of the other three species, which suggests that only one parental species (S. major) predominantly participates in backcrosses. Phenotypic hybrids S. fulvus x S. major and S. major x S. pygmaeus) were reliably identified using RAPD-PCR of nuclear DNA. However, we could find no significant traces of hybridization in S. major with alien mitotypes. Analysis of p53 pseudogenes of S. major and S. fulvus that were for the first time described in the present study produced similar results: 59 out of 60 individuals of S. major (including S. major with S. fulvus mitotypes) had only the pseudogene variant specific for S. major. This situation is possible even at low hybridization frequencies (less than 1% according to field observations and 1.4 to 2.7% according to nuclear DNA analysis) if dispersal of S. major from the sympatric zones mainly involved animals that obtained alien mtDNA via backcrossing. The prevalence of animals with alien mitotypes in some S. major populations can be explained by the founder effect. Further studies based on large samples are required for clarifying the discrepancies between mitochondrial and nuclear DNA data.     

Mitochondrial Genetic Variation in Chinese Pigs and Wild Boars

The mitochondrial DNAs (mtDNAs) from 30 pig breeds (29 Chinese native breeds and 1 European breed) and wild boars were investigated for restriction fragment length polymorphisms (RFLPs) to determine the phylogenetic relationships and genetic diversity among pig breeds and wild boars. Of the 24 enzymes used, 8 (AvaI, BclI, BglII, EcoRI, EcoRV, ScaI, StuI, and XbaI) detected polymorphisms. By combining the cleavage patterns for each enzyme, 108 individuals were sorted into eight mtDNA mitotypes. There are two haplotype lineages in domestic pigs, i.e., Chinese and European lineages. The pairwise nucleotide sequence divergence was calculated to be 0.56% between Chinese pigs and European pigs, suggesting that they might have diverged from a common ancestor approximately 280,000 years ago. The wild boars showed more extensive genetic variation, four mitotypes were detected in six wild boars. In addition, one of the Zhejiang wild boars was found to share the same mitotype with Chinese native pigs. A UPGMA tree based on genetic distance among mitotypes indicated that mtDNAs of Chinese pigs and European pigs are clearly divided into two clusters, and Chinese wild boars are more closely related to the Chinese pigs. Our results provide molecular evidence to support the previous hypothesis that pigs may be derived from two maternal origins, Asian and European wild boars. Chinese native pig breeds may have a single origin.     

Phylogeography of Pinus tabulaeformis Carr. (Pinaceae), a dominant species of coniferous forest in northern China

How coniferous trees in northern China changed their distribution ranges in response to Quaternary climatic oscillations remains largely unknown. Here we report a study of the phylogeography of Pinus tabulaeformis, an endemic and dominant species of coniferous forest in northern China. We examined sequence variation of maternally inherited, seed‐dispersed mitochondrial DNA (mtDNA) (nad5 intron 1 and nad4/3–4) and paternally inherited, pollen‐ and seed‐dispersed chloroplast DNA (cpDNA) (rpl16 and trnS‐trnG) within and among 30 natural populations across the entire range of the species. Six mitotypes and five chlorotypes were recovered among 291 trees surveyed. Population divergence was high for mtDNA variation (G_ST = 0.738, N_ST = 0.771) indicating low levels of seed‐based gene flow and significant phylogeographical structure (N_ST > G_ST, P < 0.05). The spatial distribution of mitotypes suggests that five distinct population groups exist in the species: one in the west comprising seven populations, a second with a north–central distribution comprising 15 populations, a third with a southern and easterly distribution comprising five populations, a fourth comprising one central and one western population, and a fifth comprising a single population located in the north‐central part of the species’ range. Each group apart from the fourth group is characterized by a distinct mitotype, with other mitotypes, if present, occurring at low frequency. It is suggested, therefore, that most members of each group apart from Group 4 are derived from ancestors that occupied different isolated refugia in a previous period of range fragmentation of the species, possibly at the time of the Last Glacial Maximum. Possible locations for these refugia are suggested. A comparison of mitotype diversity between northern and southern subgroups within the north‐central group of populations (Group 2) showed much greater uniformity in the northern part of the range both within and between populations. This could indicate a northward migration of the species from a southern refugium in this region during the postglacial period, although alternative explanations cannot be ruled out. Two chlorotypes were distributed across the geographical range of the species, resulting in lower levels of among‐population chlorotype variation. The geographical pattern of variation for all five chlorotypes provided some indication of the species surviving past glaciations in more than one refugium, although differentiation was much less marked, presumably due to the greater dispersal of cpDNA via pollen.