Conflicting patterns of mitochondrial and nuclear DNA diversity in Phylloscopus warblers

Molecular variation is often used to infer the demographic history of species, but sometimes the complexity of species history can make such inference difficult. The willow warbler, Phylloscopus trochilus, shows substantially less geographical variation than the chiffchaff, Phylloscopus collybita, both in morphology and in mitochondrial DNA (mtDNA) divergence. We therefore predicted that the willow warbler should harbour less nuclear DNA diversity than the chiffchaff. We analysed sequence data obtained from multiple samples of willow warblers and chiffchaffs for the mtDNA cytochrome b gene and four nuclear genes. We confirmed that the mtDNA diversity among willow warblers is low (pi = 0.0021). Sequence data from three nuclear genes (CHD-Z, AFLP-WW1 and MC1R) not linked to the mitochondria demonstrated unexpectedly high nucleotide diversity (pi values of 0.0172, 0.0141 and 0.0038) in the willow warbler, on average higher than the nucleotide diversity for the chiffchaff (pi values of 0.0025, 0.0017 and 0.0139). In willow warblers, Tajima's D analyses showed that the mtDNA diversity, but not the nuclear DNA diversity, has been reduced relative to the neutral expectation of molecular evolution, suggesting the action of a selective sweep affecting the maternally inherited genes. The large nuclear diversity seen within willow warblers is not compatible with processes of neutral evolution occurring in a population with a constant population size, unless the long-term effective population size has been very large (N(e) > 10(6)). We suggest that the contrasting patterns of genetic diversity in the willow warbler may reflect a more complex evolutionary history, possibly including historical demographic fluctuations or historical male-biased introgression of nuclear genes from a differentiated population of Phylloscopus warblers.     

Low mitochondrial DNA variation and recent colonization of Scandinavia by the wood lemming Myopus schisticolor

The population genetic structure of wood lemmings ( Myopus schisticolor ) from Scandinavia, Finland and western Siberia was examined by restriction fragment length polymorphism of mitochondrial DNA (mtDNA) in 45 individuals from six localities. The 12 observed mtDNA haplotypes demonstrated a distinct phylogeographic pattern, suggesting that the postglacial colonization of Scandinavia by wood lemmings occurred from north-east. However, a very low level of haplotype and nucleotide diversity and a lack of geographical structure were found within Scandinavia. The limited mtDNA diversity in the Scandinavian populations probably reflects recent divergence in situ after colonization by a limited number of founders. Allozyme data support this scenario.     

Armadillos exhibit less genetic polymorphism in North America than in South America: nuclear and mitochondrial data confirm a founder effect in Dasypus novemcinctus (Xenarthra)

Heterozygosity at eight nuclear enzymatic loci and mitochondrial DNA control region (D-loop) sequence polymorphism was compared between North and South American nine-banded armadillos (Dasypus novemcinctus: Xenarthra, Dasypodidae). All markers revealed a striking genetic homogeneity amongst Texas, Louisiana, and Mississippi individuals, vs. the usual level of polymorphism for the French Guiana population. This may reflect a founder effect during colonization of North America. Occurrence of polymorphism in the D-loop microsatellite motif of North American armadillos suggests a recent recovery of mitochondrial variability. Phylogeographic analyses using Dasypus kappleri as outgroup provides evidence for a clear separation between North and South American control region haplotypes.     

Genetic consequences of glacial survival and postglacial colonization in Norway spruce: combined analysis of mitochondrial DNA and fossil pollen

Norway spruce (Picea abies [L.] Karst.) is a broadly distributed European conifer tree whose history has been intensively studied by means of fossil records to infer the location of full‐glacial refugia and the main routes of postglacial colonization. Here we use recently compiled fossil pollen data as a template to examine how past demographic events have influenced the species’ modern genetic diversity. Variation was assessed in the mitochondrial nad1 gene containing two minisatellite regions. Among the 369 populations (4876 trees) assayed, 28 mitochondrial variants were identified. The patterns of population subdivision superimposed on interpolated fossil pollen distributions indicate that survival in separate refugia and postglacial colonization has led to significant structuring of genetic variation in the southern range of the species. The populations in the northern range, on the other hand, showed a shallow genetic structure consistent with the fossil pollen data, suggesting that the vast northern range was colonized from a single refugium. Although the genetic diversity decreased away from the putative refugia, there were large differences between different colonization routes. In the Alps, the diversity decreased over short distances, probably as a result of population bottlenecks caused by the presence of competing tree species. In northern Europe, the diversity was maintained across large areas, corroborating fossil pollen data in suggesting that colonization took place at high population densities. The genetic diversity increased north of the Carpathians, probably as a result of admixture of expanding populations from two separate refugia.     

Behavioural vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male-biased dispersal in a Holarctic sea duck

Genetic studies of waterfowl (Anatidae) have observed the full spectrum of mitochondrial (mt) DNA population divergence, from apparent panmixia to deep, reciprocally monophyletic lineages. Yet, these studies often found weak or no nuclear (nu) DNA structure, which was often attributed to male‐biased gene flow, a common behaviour within this family. An alternative explanation for this ‘conflict’ is that the smaller effective population size and faster sorting rate of mtDNA relative to nuDNA lead to different signals of population structure. We tested these alternatives by sequencing 12 nuDNA introns for a Holarctic pair of waterfowl subspecies, the European goosander (Mergus merganser merganser) and the North American common merganser (M. m. americanus), which exhibit strong population structure in mtDNA. We inferred effective population sizes, gene flow and divergence times from published mtDNA sequences and simulated expected differentiation for nuDNA based on those histories. Between Europe and North America, nuDNA Ф_ST was 3.4‐fold lower than mtDNA Ф_ST, a result consistent with differences in sorting rates. However, despite geographically structured and monophyletic mtDNA lineages within continents, nuDNA Ф_ST values were generally zero and significantly lower than predicted. This between‐ and within‐continent contrast held when comparing mtDNA and nuDNA among published studies of ducks. Thus, male‐mediated gene flow is a better explanation than slower sorting rates for limited nuDNA differentiation within continents, which is also supported by nonmolecular data. This study illustrates the value of quantitatively testing discrepancies between mtDNA and nuDNA to reject the null hypothesis that conflict simply reflects different sorting rates.     

线粒体DNA nad1序列在青海云杉青藏高原台面和周边地区种群中的变异

青藏高原是气候变迁的敏感区。但第四纪以来全球气候的反复变化对该地区植物分布格局的影响至今未进行过仔细研究。线粒体DNA在松科植物中是母系遗传,其变异被广泛用于研究该科植物历史上由于气候变迁造成的瓶颈作用以及冰期后扩张中形成的奠基者效应。对青海云杉位于青藏高原核心、其边缘甘肃和宁夏地区共12个种群155个个体的线粒体nad 1片段的全序列进行测序,研究该序列在各种群中的变异状况。通过测序发现该片段在青海云杉中十分保守,在所有个体中仅发现由于重复序列造成的5种单倍型(H ap A,H ap B,H ap C,H ap D和H ap E)。高原核心的所有种群均只有H ap A,而所有的4种单倍型都在高原边缘的甘肃地区存在,但这一地区仍然是H ap A占优势;但是在远离高原的宁夏地区则存在5种单倍性;多样性的变异趋势是宁夏地区高于高原边缘的甘肃地区,而甘肃地区又显著高于高原核心地区。这一结果表明,在过去气候变迁过程中,不同地区的青海云杉种群经历了不同的气候影响,这种影响造成的奠基者效应或者瓶颈作用是造成目前这种遗传多样性分布格局的主要原因。现有的单倍型分布格局,特别是高原上所有间断分布种群拥有相同的单倍型表明,森林回迁中的奠基者效应应是更为重要的因素。     

Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers

Abstract.— We examined genetic variation at 21 polymorphic allozyme loci, 15 nuclear DNA loci, and mitochondrial DNA in four spawning populations of sockeye salmon ( Oncorhynchus nerka ) from Cook Inlet, Alaska, to test for differences in the patterns of divergence among different types of markers. We were specifically interested in testing the suggestion that natural selection at allozyme loci compromises the effectiveness of these markers for describing the amount and patterns of gene flow among populations. We found concordance among markers in the amount of genetic variation within and among populations, with the striking exception of one allozyme locus ( sAH ), which exhibited more than three times the amount of among-population differentiation as other loci. A consideration of reports of discordance between allozymes and other loci indicates that these differences usually result from one or two exceptional loci. We conclude that it is important to examine many loci when estimating genetic differentiation to infer historical amounts of gene flow and patterns of genetic exchange among populations. It is less important whether those loci are allozymes or nuclear DNA markers.     

Range‐wide genetic homogeneity in the California sea mussel (Mytilus californianus): a comparison of allozymes,nuclear DNA markers,and mitochondrial DNA sequences

We tested for genetic differentiation among six populations of California sea mussels (Mytilus californianus) sampled across 4000 km of its geographical range by comparing patterns of variation at four independent types of genetic markers: allozymes, single‐copy nuclear DNA markers, and DNA sequences from the male and female mitochondrial genomes. Despite our extensive sampling and genotyping efforts, we detected no significant differences among localities and no signal of isolation by distance suggesting that M. californianus is genetically homogeneous throughout its range. This concordance differs from similar studies on other mytilids, especially in the role of postsettlement selection generating differences between exposed coastal and estuarine habitats. To assess if this homogeneity was due to M. californianus not inhabiting estuarine environments, we reviewed studies comparing allozymes with other classes of nuclear DNA markers. Although both types of markers gave broadly consistent results, there was a bias favouring studies in which allozymes were more divergent than DNA markers (nine to three) and a disproportionate number of these cases involved marine taxa (seven). Furthermore, allozymes were significantly more heterogeneous than DNA markers in three of the four studies that sampled coastal and estuarine habitats. We conclude that the genetic uniformity exhibited by M. californianus may result from a combination of extensive gene flow and the lack of exposure to strong selective gradients across its range.     

DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis)

Uniparentally inherited mitochondrial (mt)DNA and chloroplast (cp)DNA microsatellites (cpSSRs) were used to examine population genetic structure and biogeographic patterns of bird-dispersed seed and wind-disseminated pollen of whitebark pine (Pinus albicaulis Engelm.). Sampling was conducted from 41 populations throughout the range of the species. Analyses provide evidence for an ancestral haplotype and two derived mtDNA haplotypes with distinct regional distributions. An abrupt contact zone between mtDNA haplotypes in the Cascade Range suggests postglacial biogeographic movements. Among three cpSSR loci, 42 haplotypes were detected within 28 cpSSR sample populations that were aggregated into six regions. Analysis of molecular variance (amova) was used to determine the hierarchical genetic structure of cpSSRs. amova and population pairwise comparisons (FST ) of cpSSR, and geographical distribution of mtDNA haplotypes provide insights into historical changes in biogeography. The genetic data suggest that whitebark pine has been intimately tied to climatic change and associated glaciation, which has led to range movements facilitated by seed dispersal by Clark's nutcracker (Nucifraga columbiana Wilson). The two hypotheses proposed to explain the genetic structure are: (i) a northward expansion into Canada and the northern Cascades in the early Holocene; and (ii) historical gene flow between Idaho and the Oregon Cascades when more continuous habitat existed in Central Oregon during the late Pleistocene. Genetic structure and insights gained from historical seed movements provide a basis on which to develop recovery plans for a species that is at risk from multiple threats.     

Natural hybridization of Yezo and Sakhalin spruce in central Hokkaido,revealed by DNA markers with contrasting modes of inheritance

Yezo spruce (Picea jezoensis var. jezoensis) and Sakhalin spruce (Picea glehnii) occur across Hokkaido and co‐occur in some forest habitats. This leads to the potential for natural hybridization between these two species, which has been shown to occur at low frequencies. The purpose of this study was to identify these hybrids and their possible mating patterns, using various Pinaceae DNA markers with different modes of inheritance. The markers used were maternally inherited mitochondrial DNA (mtDNA), paternally inherited chloroplast DNA (cpDNA) and biparentally inherited nuclear microsatellites (nSSRs). Seven putative natural hybrids, four artificially‐crossed F₁ hybrids, four parent plants from each species, and two artificially‐backcrossed hybrids of putative natural hybrids and their parents were analyzed using the diagnostic DNA markers developed in this study. We found Yezo spruce and Sakhalin spruce to be distinct (J and G types, respectively), and the modes of inheritance held true for the two species, as was previously reported to be the case in Pinaceae. Four of the seven putative natural hybrids harbored J‐type cpDNA, G‐type mtDNA and J/G‐type nSSRs, indicating that natural F₁ hybrids are likely to arise from a G (female) × J (male) crossing. One natural hybrid harbored G‐type cpDNA, J‐type mtDNA and J/G‐type nSSRs, which implies that hybrids produced by J (female) × G (male) crossings occur at low frequencies. The two remaining hybrids harbored J‐type cpDNA and mtDNA with either J/G or J/J‐type nSSRs, suggesting that they may be F₂ hybrids resulting from backcrossing between an F₁ hybrid and a Yezo spruce.     

Imprint of post-glacial history in a narrowly distributed endemic spruce, Picea alcoquiana, in central Japan observed in nuclear microsatellites and organelle DNA markers

Aim We aim to infer the post‐glacial history of the narrowly distributed endemic spruce Picea alcoquiana in Japan, and to assess the hypothesis that the existing narrow natural range of the species has resulted from the diminution of the past natural range since the last glacial period. Location Mountainous forests in central Honshu Island in Japan. Methods We assessed the geographical patterns of genetic variation across nine populations of P. alcoquiana across its natural range using five nuclear microsatellites and polymerase chain reaction–restriction fragment length polymorphism markers for chloroplast (cp) and mitochondrial (mt) DNA. This study focuses on the genetic differentiation between northern peripherally isolated and southern core populations within the natural range of the species in central Honshu. In addition, based on diagnostic morphological traits of the cone, we used reliable macrofossil evidence to gain further insight into the past natural range of the species. Results Picea alcoquiana shows a level of genetic differentiation among populations (Φ_ST = 0.082) that was higher than the levels observed in nuclear microsatellites for other anemophilous and widespread tree species in Japan. A notable finding for the nuclear microsatellites was the loss of rare alleles and strong evidence of a recent bottleneck in the peripherally isolated populations. Analysis of molecular variance in cpDNA and mtDNA markers showed an absence of genetic differentiation between the peripherally isolated and core populations. Macrofossil evidence indicated that the past natural range of the species extended to a lower elevation and c. 135 km north of the existing peripherally isolated populations during the last glacial period (c. 28,000 yr bp ). Main conclusions During the last glacial period, P. alcoquiana had a wider natural range in which the peripherally isolated and core populations could have been geographically continuous with each other, and effective gene flow by means of pollen and seeds might have occurred. The recent bottleneck and consequent loss of rare alleles in the peripherally isolated populations might have evolved during the diminution and retreat of the northern part of the past natural range southwards to the core area and during the subsequent separation of the peripherally isolated populations from the core area since the last glacial period.     

Phylogenetic estimation of Mytilidae in the East China Sea inferred from mitochondrial genes and nuclear DNA sequence variation

We performed a phylogenetic estimation of the family Mytilidae in the East China Sea based on nuclear internal transcribed spacer (ITS) genes and two mitochondrial genes (COI and 16S RNA). Analysis of five mytilid species based on each of the three genes resulted in mostly congruent trees, although there were some discrepancies in the classification of these species. We combine the results obtained from the three separate analyses to provide a phylogenetic estimation of Mytilidae. We found that the Mytilidae was divided into two major lineages: in one clade, Mytilus galloprovincialis was grouped with Mytilus coruscus; in the second clade, Septifer bilocularis was placed at the basal position in an individual clade, and Perna viridis and Musculista senhousia were recovered as a monophyletic group. Although these finding provide important insights into the taxonomic relationships among the Mytilidae, many aspects of Mytilidae phylogeny remain unresolved. Further analysis based on more molecular information and extensive taxon sampling is necessary to elucidate the phylogenetic relationships among the major lineages within the Mytilidae.     

Analysis of genetic diversity of domestic cattle in East and Southeast Asia in terms of variations in restriction sites and sequences of mitochondrial DNA

There are three major groups of domestic cattle in East and Southeast Asia: European cattle, Zebu cattle, and Bali cattle. Ten restriction enzymes were used to analyze restriction site variants in the mitochondrial DNA (mtDNA) in 178 individuals belonging to these three groups of cattle. The results indicate that each of the three groups has mtDNA with a specific haplotype. The sequence of the mitochondrial gene for cytochrome b in representative haplotypes of Zebu and Bali cattle was determined and was compared with that of European cattle in the literature. We calculated 51 pairwise nucleotide sequence differences between European and Zebu cattle and 91 between European and Bali cattle. Our results suggest that ancestral populations of Asiatic domestic cattle may have diverged into two lineages—Bali and European plus Zebu—more than 3 million years ago, and then the European and Zebu groups diverged more than 1 million years or so before domestication occurred.The sequences of mitochondrial genes for cytochrome b from Zebu cattle, Bali cattle and Water buffalo will appear in the DDBJ, EMBL and GenBank nucleotide sequence databases, with the following accession numbers: D34635, D34636 and D34637.     

A tale of two genomes: contrasting patterns of phylogeographic structure in a widely distributed bat

One of the most widely distributed bats in the New World, the big brown bat (Eptesicus fuscus) exhibits well-documented geographic variation in morphology and life history traits, suggesting the potential for significant phylogeographic structure as well as adaptive differentiation among populations. In a pattern broadly consistent with morphologically defined subspecies, we found deeply divergent mitochondrial lineages restricted to different geographic regions. In contrast, sequence data from two nuclear loci suggest a general lack of regional genetic structure except for peripheral populations in the Caribbean and Mexico/South America. Coalescent analyses suggest that the striking difference in population structure between genomes cannot be attributed solely to different rates of lineage sorting, but is likely due to male-mediated gene flow homogenizing nuclear genetic diversity across most of the continental range. Despite this ongoing gene flow, selection has apparently been effective in producing and maintaining adaptive differentiation among populations, while strong female site fidelity, maintained over the course of millions of years, has produced remarkably deep divergence among geographically isolated matrilines. Our results highlight the importance of evaluating multiple genetic markers for a more complete understanding of population structure and history.     

General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics

To choose one or more appropriate molecular markers or gene regions for resolving a particular systematic question among the organisms at a certain categorical level is still a very difficult process. The primary goal of this review, therefore, is to provide a theoretical information in choosing one or more molecular markers or gene regions by illustrating general properties and phylogenetic utilities of nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) that have been most commonly used for phylogenetic researches. The highly conserved molecular markers and/or gene regions are useful for investigating phylogenetic relationships at higher categorical levels (deep branches of evolutionary history). On the other hand, the hypervariable molecular markers and/or gene regions are useful for elucidating phylogenetic relationships at lower categorical levels (recently diverged branches). In summary, different selective forces have led to the evolution of various molecular markers or gene regions with varying degrees of sequence conservation. Thus, appropriate molecular markers or gene regions should be chosen with even greater caution to deduce true phylogenetic relationships over a broad taxonomic spectrum.     

Genetic population structure and mobility of two nectar-feeding bats from Venezuelan deserts: inferences from mitochondrial DNA

Glossophaga longirostris and Leptonycteris curasoae are nectar-feeding bats associated with arid zones in northern South America. Despite their close phylogenetic relationship, sympatric condition and niche similarities, morphological and ecological evidence suggest that these species differ in dispersal capabilities. Using mitochondrial DNA, we tested the hypothesis that these species exhibit different levels of population structure that are congruent with their particular movement capabilities. We sequenced a section of the control region of mtDNA for 41 G. longirostris and 42 L. curasoae from 11 zones in Venezuela. Population subdivision in G. longirostris (FST = 0.725) was considerably higher than in L. curasoae (FST = 0.167). L. curasoae individuals shared haplotypes at greater distances (812 km) than G. longirostris (592 km). Our results offer preliminary evidence for one of two possible scenarios, either greater mobility in L. curasoae or a higher degree of female philopatry in G. longirostris.     

A long-term record of carbon exchange in a boreal black spruce forest: means, responses to interannual variability, and decadal trends

We present a decadal (1994–2004) record of carbon dioxide flux in a 160‐year‐old black spruce forest/veneer bog complex in central Manitoba, Canada. The ecosystem shifted from a source (+41 g C m⁻², 1995) to a sink (−21 g C m⁻², 2004) of CO₂ over the decade, with an average net carbon balance near zero. Annual mean temperatures increased 1–2° during the period, consistent with the decadal trend across the North American boreal biome. We found that ecosystem carbon exchange responded strongly to air temperature, moisture status, potential evapotranspiration, and summertime solar radiation. The seasonal cycle of ecosystem respiration significantly lagged that of photosynthesis, limited by the rate of soil thaw and the slow drainage of the soil column. Factors acting over long time scales, especially water table depth, strongly influenced the carbon budget on annual time scales. Net uptake was enhanced and respiration inhibited by multiple years of rainfall in excess of evaporative demand. Contrary to expectations, we observed no correlation between longer growing seasons and net uptake, possibly because of offsetting increases in ecosystem respiration. The results indicate that the interactions between soil thaw and water table depth provide critical controls on carbon exchange in boreal forests underlain by peat, on seasonal to decadal time scales, and these factors must be simulated in terrestrial biosphere models to predict response of these regions to future climate.     

Cytoplasmic male sterility and fertility restoration in wheat are not associated with rearrangements of mitochondrial DNA in the gene regions for cob,coxII, or coxI

In comparing the genetic organization and exploring the molecular basis of cytoplasmic male sterility (CMS) in wheat, mitochondrial DNAs (mtDNA) from Triticum aestivum, T. timopheevi, CMS alloplasmic wheat with T. aestivum nucleus and T. timopheevi mitochondria, and fertility-restored lines were compared by hybridization analysis with specific probes for three gene regions: CoxII, cob, and coxI. Minor differences between T. aestivum- and T. timopheevi-derived sources were found for gene regions for coxII and cob. For coxI, there are significant differences between T. timopheevi-derived mtDNAs and T. aestivum mtDNA extending beyond an 8 kb distance. All T. timopheevi-derived mtDNA sources have a chimeric gene region (orf256) with part of the upstream coxI gene region, including some coxI-coding region, preceding coxI. The part of orf256 that does not include any of coxI and the 3-flanking region of CMS coxI are not found in T. aestivum mtDNA. Neither orf256 nor the CMS 3-flanking region of coxI are found in T. timopheevi or T. aestivum chloroplastic or nuclear DNA. There do not appear to be DNA sequence differences for the three gene regions studied that are related to either CMS or fertility-restored states.     

Doubly uniparental inheritance of mitochondrial DNA in freshwater mussels: History and status of the European species

Doubly uniparental inheritance (DUI) is a mode of inheriting mitochondrial DNA that is distinct from strictly maternal inheritance. It has been described in nine and three families of marine and freshwater mussels, respectively, including the European margaritiferids and unionids. Among the 16 freshwater species of Unionida inhabiting Europe, DUI has been described in 9 species of dioecious mussels and was absent from a single hermaphroditic species and from secondary hermaphroditic specimens. The DUI freshwater mussels include two vastly genetically different mitochondrial genomes: maternal (F genome) and paternal (M genome), which coexist within the same specimen but in different tissues. The F genome is present in all female tissues and somatic male tissues. It is inherited in the typical, maternal, manner. Conversely, the M genome is located primarily in the male gonads and generative cells, and is inherited paternally. Dioecious Unionidae display unique characteristics that have been interrelated for over 200 million years: a high fidelity of the transmission of the F and M genomes in DUI and two paths of spermatogenesis–the typical path that produces sperm cells containing mitochondria with the F genome and the atypical path that produces sperm cells with the M genome. The mitogenomes of freshwater mussels display unique features that are not present in any other animal, that is, an additional, gender-specific gene and an elongated cox2 gene occurring exclusively in the M genome. These features mean that the mitochondria, in addition to their basic function of producing energy, also may take part in determining sex in these dioecious organisms.