Origin and history of mitochondrial DNA lineages in domestic horses

Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.     

Association between chloroplast and mitochondrial lineages in oaks

Patterns of chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) variation were studied in 378 populations of oak trees sampled throughout the southern half of France. Six cpDNA haplotypes detected in a previous European survey and three new cpDNA haplotypes were found in this region. Two mitochondrial polymorphisms detected earlier by restriction analysis of PCR-amplified fragments alone, or in combination with single-strand conformation polymorphism (SSCP), were compared with the cpDNA data. Sequencing revealed the nature of the two mitochondrial mutations: a single-base substitution and a 4-bp inversion associated with a 22-bp hairpin secondary structure. The single-base substitution was then analyzed by allele-specific amplification. Results for the two cytoplasmic genomes were combined, which allowed the identification of 12 cpDNA-mtDNA haplotypes. The 4-bp mtDNA inversion has appeared independently in different cpDNA lineages. Given the peculiar nature of this mtDNA mutation, we suggest that intramolecular recombination leading to repeated inversions of the 4-bp sequence (rather than paternal leakage of one of the two genomes) is responsible for this pattern. Furthermore, the geographic locations of the unusual cpDNA-mtDNA associations (due to the inversion) usually do not match the zones of contact between divergent haplotypes. In addition, in southern France, the groupings of populations based on the mtDNA substitution were strictly congruent with those based on cpDNA. Because many populations that are polymorphic for both cpDNA and mtDNA have remained in contact since postglacial recolonization in this area without producing any new combination of cytoplasms involving the mitochondrial substitution, we conclude that paternal leakage is not a significant factor at this timescale. Such results confirm and expand our earlier conclusions based on controlled crosses.      

Numerous mitochondrial DNA haplotypes reveal multiple independent polyploidy origins of hexaploids in Carassius species complex

Evolutionary trajectory and occurrence history of polyploidy have been extensively studied in plants, but they remain quite elusive in vertebrates. Here, we sampled and gathered 4,159 specimens of polyploid Carassius species complex including 1,336 tetraploids and 2,823 hexaploids from a large geographic scale (49 localities) across East Asia, and identified a huge number of 427 diverse haplotypes of mitochondrial control region, in which 74 haplotypes with total occurrence frequency up to 75.498% were shared by hexaploids and tetraploids. Significantly, these diverse haplotypes were clustered into four major lineages, and many haplotypes of hexaploids and tetraploids were intermixed in every lineage. Moreover, the evolutionary trajectory and occurrence history of four different lineages were revealed by a simplified time‐calibrated phylogenetic tree, and their geographic distribution frequencies and haplotype diversity were also analyzed. Furthermore, lineage C and D were revealed to undergo population expansion throughout mainland China. Therefore, our current data indicate that hexaploids should undergo multiple independent polyploidy origins from sympatric tetraploids in the polyploid Carassius species complex across East Asia.     

Phylogenetic and biogeographic implications of chloroplast DNA variation in Picea

Purified chloroplast DNA ( cp DNA) extracts from 31 species of Picea and two species of Pinus (P. sylvestris and P. cembra ) were digested with eight restriction endo-nucleases, separated by electrophoresis and scored for restriction fragment length polymorphisms. The resulting data was analyzed phenetically and cladistically. The phenetic analysis indicated lower levels of cpDNA differentiation within Picea than within Pinus and lower levels of differentiation among Eurasian than among North-American Picea species. The cladistic analysis, using Pinus sylvestris as an outgroup, suggested monophyly for Picea and resolved several monophyletic groups among the 31 species of Picea . An assessment of biogeographic events, based on the cladogram, suggests that Picea originated in North-America and that the colonization of Eurasia occurred through separate, intercontinental migrations.     

Evidence for biogeographic patterning of mitochondrial DNA sequences in Eastern horse populations

Equine mitochondrial DNA (mtDNA) phylogeny reconstruction reveals a complex pattern of variation unlike that seen in other large domesticates. It is likely that this pattern reflects a process of multiple and repeated, although not necessarily independent, domestication events. Until now, no clear geographic affiliation of clades has been apparent. In this study, amova analyses have revealed a significant non-random distribution of the diversity among equine populations when seven newly sequenced Eurasian populations were examined in the context of previously published sequences. The association of Eastern mtDNA types in haplogroup F was highly significant using Fisher's exact test of independence (P = 0.00000). For the first time, clear biogeographic partitioning has been detected in equine mtDNA sequence.     

人类线粒体DNA世系的系统发育关系研究

本文以人类线粒体DNA为例,回顾了其系统发育关系的重建的研究历史,进而总结介绍了该分析方法在人类进化历史研究、线粒体DNA数据质量评估以及疾病相关线粒体DNA突变的甄别等方面的应用,以期对该方法在国内的推广应用有所裨益。     

Evolutionary relationships among the male and female mitochondrial DNA lineages in the Mytilus edulis species complex

A novel form of mitochondrial DNA (mtDNA) inheritance has previously been documented for the blue mussel (Mytilus edulis). Female mussels inherit their mtDNA solely from their mother while males inherit mtDNA from both their mother and their father. In males, the paternal mtDNA is preferentially amplified so that the male gonad is highly enriched for the paternal mtDNA that is then transmitted from fathers to sons. We demonstrate that this mode of mtDNA inheritance also operates in the closely related species M. galloprovincialis and M. trossulus. The evolutionary relationship between the male and female mtDNA lineages is estimated by phylogenetic analysis of 455 nucleotides from the large subunit ribosomal RNA gene. We have found that the male and female lineages are highly divergent; the divergence of these lineages began prior to the speciation of the three species of blue mussels. Further, the separation between the male and female lineages is estimated to have occurred between 5.3 and 5.7 MYA.      

Glacial history of the European marine mussels Mytilus,inferred from distribution of mitochondrial DNA lineages

Mussels of the genus Mytilus have been used to assess the circumglacial phylogeography of the intertidal zone. These mussels are representative components of the intertidal zone and have rapidly evolving mitochondrial DNA, suitable for high resolution phylogeographic analyses. In Europe, the three Mytilus species currently share mitochondrial haplotypes, owing to the cases of extensive genetic introgression. Genetic diversity of Mytilus edulis, Mytilus trossulus and Mytilus galloprovincialis was studied using a 900-bp long part of the most variable fragment of the control region from one of their two mitochondrial genomes. To this end, 985 specimens were sampled along the European coasts, at sites ranging from the Black Sea to the White Sea. The relevant DNA fragments were amplified, sequenced and analyzed. Contrary to the earlier findings, our coalescence and nested cladistics results show that only a single M. edulis glacial refugium existed in the Atlantic. Despite that, the species survived the glaciation retaining much of its diversity. Unsurprisingly, M. galloprovincialis survived in the Mediterranean Sea. In a relatively short time period, around the climatic optimum at 10 ky ago, the species underwent rapid expansion coupled with population differentiation. Following the expansion, further contemporary gene flow between populations was limited.     

High variability of chloroplast DNA in three Mediterranean evergreen oaks indicates complex evolutionary history

Chloroplast DNA variation was studied in three evergreen Quercus species (Q. suber L., Q. ilex L. and Q. coccifera L.) from the Western Mediterranean Basin using PCR-RFLP. We studied five primer pair/enzyme combinations, four of them previously used in other European Quercus, obtaining a large number of haplotypes (81) grouped in three main types (suber type, ilex-coccifera I type and ilex-coccifera II type). Such level of haplotype diversity is higher than previously reported for the genus. Remarkable differences in haplotype richness between species have been found. Q. ilex and Q. coccifera usually share the same haplotypes, while a number of Q. suber populations possesses variants of the ilex-coccifera I type. This fact is interpreted as a result of genetic introgression between Q. suber and Q. ilex. Reproductive factors that could determine this exchange are discussed, as well as the influence of different species histories on the present structure of evergreen Quercus in the Western Mediterranean Basin.     

Deep common ancestry of indian and western-Eurasian mitochondrial DNA lineages

About a fifth of the human gene pool belongs largely either to Indo-European or Dravidic speaking people inhabiting the Indian peninsula. The 'Caucasoid share' in their gene pool is thought to be related predominantly to the Indo-European speakers. A commonly held hypothesis, albeit not the only one, suggests a massive Indo-Aryan invasion to India some 4,000 years ago [1]. Recent limited analysis of maternally inherited mitochondrial DNA (mtDNA) of Indian populations has been interpreted as supporting this concept [2] [3]. Here, this interpretation is questioned. We found an extensive deep late Pleistocene genetic link between contemporary Europeans and Indians, provided by the mtDNA haplogroup U, which encompasses roughly a fifth of mtDNA lineages of both populations. Our estimate for this split is close to the suggested time for the peopling of Asia and the first expansion of anatomically modern humans in Eurasia [4] [5] [6] [7] [8] and likely pre-dates their spread to Europe. Only a small fraction of the 'Caucasoid-specific' mtDNA lineages found in Indian populations can be ascribed to a relatively recent admixture.     

Lineage sorting accounting for the disassociation between chloroplast and mitochondrial lineages in oaks of southern France.

Dumolin-Lapégue et al. (Mol. Biol. Evol. 15: 1321-1331. 1998) suggested that recurrent inversions of a 4-bp sequence of the mtDNA nad4-1/2 locus due to intramolecular recombination were responsible for the disassociation of chloroplast and mitochondrial genomes of French oaks. Based on their PCR-RFLP (PCR-restriction fragment length polymorphism) data obtained from three noncoding spacers, a minimum spanning network representing the phylogeny of the cpDNA was reconstructed. The mapping of alleles b and c of the mtDNA nad4-1/2 locus on the cpDNA network revealed a nonrandom distribution, which contradicted the expected patterns when repeated, and ongoing inversions had been occurring. The fact that polymorphisms (a mixed c + d type) were mostly restricted to the interior nodes of the network, which represented ancient haplotypes and geographically coincided with probable glacial refugia in southern Europe, agreed with a migrant-pool model. Evidence of a widespread pattern of polymorphism distribution indicated that mtDNA haplotypes were likely to be more ancient than the cpDNA haplotypes. Lineage sorting, due to relative age of cpDNA vs. mtDNA, plus the specific migratory mode, which recruited colonists from a random sample of resource populations during glacial expansion (thereby extending the lineage sorting period, LSP), may have resulted in the disassociation of chloroplast and mitochondrial genomes in oaks.     

Strong mitochondrial DNA support for a Cretaceous origin of modern avian lineages

Background  

Determining an absolute timescale for avian evolutionary history has proven contentious. The two sources of information available, paleontological data and inference from extant molecular genetic sequences (colloquially, 'rocks' and 'clocks'), have appeared irreconcilable; the fossil record supports a Cenozoic origin for most modern lineages, whereas molecular genetic estimates suggest that these same lineages originated deep within the Cretaceous and survived the K-Pg (Cretaceous-Paleogene; formerly Cretaceous-Tertiary or K-T) mass-extinction event. These two sources of data therefore appear to support fundamentally different models of avian evolution. The paradox has been speculated to reflect deficiencies in the fossil record, unrecognized biases in the treatment of genetic data or both. Here we attempt to explore uncertainty and limit bias entering into molecular divergence time estimates through: (i) improved taxon (n = 135) and character (n = 4594 bp mtDNA) sampling; (ii) inclusion of multiple cladistically tested internal fossil calibration points (n = 18); (iii) correction for lineage-specific rate heterogeneity using a variety of methods (n = 5); (iv) accommodation of uncertainty in tree topology; and (v) testing for possible effects of episodic evolution.     

Isolation and introgression in the Intermountain West: contrasting gene genealogies reveal the complex biogeographic history of the American pika (Ochotona princeps)

Aim We studied the history of colonization, diversification and introgression among major phylogroups in the American pika, Ochotona princeps (Lagomorpha), using comparative and statistical phylogeographic methods. Our goal was to understand how Pleistocene climatic fluctuations have shaped the distribution of diversity at mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) loci in this alpine specialist. Location North America’s Intermountain West. Methods We accumulated mtDNA sequence data (c. 560–1700 bp) from 232 pikas representing 64 localities, and sequenced two nuclear introns (mast cell growth factor, c. 550 bp, n = 148; protein kinase C iota, c. 660 bp, n = 139) from a subset of individuals. To determine the distribution of major mtDNA lineages, we conducted a phylogenetic analysis on the mtDNA sequence data, and we calculated divergence times among the lineages using a Bayesian Markov chain Monte Carlo approach. Relationships among nuclear alleles were explored with minimum spanning networks. Finally, we conducted coalescent simulations of alternative models of population history to test for congruence between nDNA and mtDNA responses to Pleistocene glacial cycles. Results We found that: (1) all individuals could be assigned to one of five allopatric mtDNA lineages; (2) lineages are associated with separate mountain provinces; (3) lineages originated from at least two rounds of differentiation; (4) nDNA and mtDNA markers exhibited overall phylogeographic congruence; and (5) introgression among phylogroups has occurred at nuclear loci since their initial isolation. Main conclusions Pika populations associated with different mountain systems have followed separate but not completely independent evolutionary trajectories through multiple glacial cycles. Range expansion associated with climate cooling (i.e. glaciations) promoted genetic admixture among populations within mountain ranges. It also permitted periodic contact and introgression between phylogroups associated with different mountain systems, the record of which is retained at nDNA but not mtDNA loci. Evidence for different histories at nuclear and mtDNA loci (i.e. periodic introgression versus deep isolation, respectively) emphasizes the importance of multilocus perspectives for reconstructing complete population histories.     

Diversity and trans-arctic invasion history of mitochondrial lineages in the North Atlantic Macoma balthica complex (Bivalvia: Tellinidae)

The history of repeated inter- or transoceanic invasions in bivalve mollusks of the circumpolar Macoma balthica complex was assessed from mtDNA COIII sequences. The data suggest that four independent trans-Arctic invasions, from the Pacific, gave rise to the current lineage diversity in the North Atlantic. Unlike in many other prominent North Atlantic littoral taxa, no evidence for (postinvasion) trans-Atlantic connections was found in the M. balthica complex. The earliest branch of the mtDNA tree is represented by the temperate-boreal North American populations (=Macoma petalum), separated from the M. balthica complex proper in the Early Pliocene at latest. The ensuing trans-Arctic invasions established the North European M. b. rubra, which now prevails on the North Sea and northeast Atlantic coasts, about two million years ago, and the currently northwest Atlantic M. balthica lineage in the Canadian Maritimes, in the Middle Pleistocene. The final reinvasion(s) introduced a lineage that now prevails in a number of North European marginal seas and is still hardly distinguishable from North Pacific mtDNA (M. b. balthica). We used coalescence simulation analyses to assess the age of the latest invasion from the Pacific to the northeast Atlantic. The results refute the hypothesis of recent, human-mediated reintroductions between northeast Pacific and the North European marginal seas in historical times. Yet they also poorly fit the alternative hypotheses of an early postglacial trans-Arctic invasion (< 11 thousand years ago), or an invasion during the previous Eemian interglacial (120 thousand years ago). Divergence time estimates rather fall in the Middle Weichselian before the Last Glacial Maximum, in conflict with the conventional thinking of trans-Arctic biogeographical connections; an early Holocene reinvasion may still be regarded as the most plausible scenario. Today, the most recently invaded Pacific mtDNA lineage is found admixed with the earlier established European Atlantic "rubra" lineage in the Baltic Sea and in Barents Sea populations east of the Varanger peninsula, and it is practically exclusive in the White and Pechora seas. Yet mtDNA does not always constitute an unequivocal taxonomic marker at individual level; the marginal populations represent hybrid swarms of the Atlantic and Pacific lineages in their nuclear genes.     

Nuclear and mitochondrial sequence data reveal the major lineages of starlings, mynas and related taxa

We investigated the phylogenetic relationships among the major lineages of the avian family Sturnidae and their placement within the Muscicapoidea clade using two nuclear (RAG-1 and myoglobin) and one mitochondrial gene (ND2). Among Muscicapoidea, we recovered three clades corresponding to the families Cinclidae, Muscicapidae and Sturnidae (sensu [Sibley, C.G., Monroe Jr., B.L., 1990. Distribution and Taxonomy of Birds of the World. Yale University Press, New Haven, CT]). Within the sturnoid lineage Mimini and Sturnini are sister groups, with Buphagus basal to them. We identified three major lineages of starlings: the Philippine endemic genus Rhabdornis, an Oriental-Australasian clade (genera Scissirostrum, Gracula, Mino, Ampeliceps, Sarcops, Aplonis), and an Afrotropical-Palaearctic clade (all African taxa, Sturnus and Acridotheres). We discuss the biogeographic implications of our findings and suggest an Asiatic origin for this family. The congruence between the age of major clades, estimated by NPRS, and palaeoclimatic data present evidence for the role of climatic changes in shaping present day distribution of the group.     

Ornament evolution in dragon lizards: multiple gains and widespread losses reveal a complex history of evolutionary change

The expression in females of ornaments thought to be the target of sexual selection in males is a long-standing puzzle. Two main hypotheses are proposed to account for the existence of conspicuous ornaments in both sexes (mutual ornamentation): genetic correlation between the sexes and sexual selection on females as well as males. We examined the pattern of ornament gains and losses in 240 species of dragon lizards (Agamidae) in order to elucidate the relative contribution of these two factors in the evolution of mutual ornamentation. In addition, we tested whether the type of shelter used by lizards to avoid predators predicts the evolutionary loss or constraint of ornament expression. We found evidence that the origin of female ornaments is broadly consistent with the predictions of the genetic correlation hypothesis. Ornaments appear congruently in both sexes with some lineages subsequently evolving male biased sexual dimorphism, apparently through the process of natural selection for reduced ornamentation in females. Nevertheless, ornaments have also frequently evolved in both sexes independently. This suggests that genetic correlations are potentially weak for several lineages and sexual selection on females is responsible for at least some evolutionary change in this group. Unexpectedly, we found that the evolutionary loss of some ornaments is concentrated more in males than females and this trend cannot be fully explained by our measures of natural selection.     

Glacial history of the North Atlantic marine snail, Littorina saxatilis, inferred from distribution of mitochondrial DNA lineages

The North Atlantic intertidal gastropod, Littorina saxatilis (Olivi, 1792), exhibits extreme morphological variation between and within geographic regions and has become a model for studies of local adaptation; yet a comprehensive analysis of the species' phylogeography is lacking. Here, we examine phylogeographic patterns of the species' populations in the North Atlantic and one remote Mediterranean population using sequence variation in a fragment of the mitochondrial cytochrome b gene (607 bp). We found that, as opposed to many other rocky intertidal species, L. saxatilis has likely had a long and continuous history in the Northwest Atlantic, including survival during the last glacial maximum (LGM), possibly in two refugia. In the Northeast Atlantic, several areas likely harboured refugial populations that recolonized different parts of this region after glacial retreat, resulting in strong population structure. However, the outlying monomorphic Venetian population is likely a recent anthropogenic introduction from northern Europe and not a remnant of an earlier wider distribution in the Mediterranean Sea. Overall, our detailed phylogeography of L. saxatilis adds an important piece to the understanding of Pleistocene history in North Atlantic marine biota as well as being the first study to describe the species' evolutionary history in its natural range. The latter contribution is noteworthy because the snail has recently become an important model species for understanding evolutionary processes of speciation; thus our work provides integral information for such endeavours.