Mitochondrial DNA Evidence Research Articles

Glacial vicariance in Eurasia: mitochondrial DNA evidence from Scots pine for a complex heritage involving genetically distinct refugia at mid-northern latitudes and in Asia Minor.

BackgroundAt the last glacial maximum, Fennoscandia was covered by an ice sheet while the tundra occupied most of the rest of northern Eurasia. More or less disjunct refugial populations of plants were dispersed in southern Europe, often trapped between mountain ranges and seas. Genetic and paleobotanical evidences indicate that these populations have contributed much to Holocene recolonization of more northern latitudes. Less supportive evidence has been found for the existence of glacial populations located closer to the ice margin. Scots pine (Pinus sylvestris L.) is a nordic conifer with a wide natural range covering much of Eurasia. Fractures in its extant genetic structure might be indicative of glacial vicariance and how different refugia contributed to the current distribution at the continental level. The population structure of Scots pine was investigated on much of its Eurasian natural range using maternally inherited mitochondrial DNA polymorphisms.ResultsA novel polymorphic region of the Scots pine mitochondrial genome has been identified, the intron 1 of nad7, with three variants caused by insertions-deletions. From 986 trees distributed among 54 populations, four distinct multi-locus mitochondrial haplotypes (mitotypes) were detected based on the three nad7 intron 1 haplotypes and two previously reported size variants for nad1 intron B/C. Population differentiation was high (GST = 0.657) and the distribution of the mitotypes was geographically highly structured, suggesting at least four genetically distinct ancestral lineages. A cosmopolitan lineage was widely distributed in much of Europe throughout eastern Asia. A previously reported lineage limited to the Iberian Peninsula was confirmed. A new geographically restricted lineage was found confined to Asia Minor. A new lineage was restricted to more northern latitudes in northeastern Europe and the Baltic region.ConclusionThe contribution of the various ancestral lineages to the current distribution of Scots pine was asymmetric and extant endemism reflected the presence of large geographic barriers to migration. The results suggest a complex biogeographical history with glacial refugia shared with temperate plant species in southern European Peninsulas and Asia Minor, and a genetically distinct glacial population located more North. These results confirm recent observations for cold tolerant species about the possible existence of refugial populations at mid-northern latitudes contributing significantly to the recolonization of northern Europe. Thus, Eurasian populations of nordic plant species might not be as genetically homogenous as assumed by simply considering them as offsets of glacial populations located in southern peninsulas. As such, they might have evolved distinctive genetic adaptations during glacial vicariance, worth evaluating and considering for conservation.

Description of a new Tityus species (Scorpiones: Buthidae) from Sierra de Portuguesa, western Venezuela, based on morphological and mitochondrial DNA evidence

Description of a new Tityus species (Scorpiones: Buthidae) from Sierra de Portuguesa, western Venezuela, based on morphological and mitochondrial DNA evidence

Novel phylogeny of the raccoon family (Procyonidae: Carnivora) based on nuclear and mitochondrial DNA evidence

The raccoon family, Procyonidae, is the least studied of the caniform (dog-like) carnivore families. Often represented by two or three species in carnivore phylogenetic studies, to date, no molecular study has focused on the procyonids themselves. The family Procyonidae is sister to Mustelidae (weasels, badgers, otters, and relatives) within the superfamily Musteloidea, which also includes the families Ailuridae (monotypic red panda, Ailurus fulgens) and Mephitidae (skunks). The Wrst complete phylogeny of the recent procyonids (Decker and Wozencraft, 1991) based on 129 morphological characters delineated two subfamilies, Potosinae and Procyoninae, which were upheld (as the tribal designations Potosini and Procyonini) in the morphology-based phylogeny of Baskin (2004), including both extant and fossil procyonids. The red panda has sometimes been included in the Procyonidae as a third subfamily (Simpson, 1945; Baskin, 1998, 2003), but while the phylogenetic aYnity of the red panda within the musteloids is unknown (Flynn et al., 2000, 2005; Delisle and Strobeck, 2005; Flynn and Wesley-Hunt, 2005; Fulton and Strobeck, 2006; Sato et al., 2006), it is no longer generally accepted as a member of the Procyonidae. The subfamily Potosinae contains two genera, Potos (kinkajou) and Bassaricyon (olingos), while Procyoninae contains three: Bassariscus (ringtails), Nasua (coatis), and Procyon (raccoons). A putative sixth genus contains the monotypic mountain coati, Nasuella olivaceae. Found only in the Andes, N. olivaceae is smaller than, but otherwise similar to, the ring-tailed coati, Nasua nasua, and is often considered a species of Nasua, rather than a distinct genus (Nowak, 1991).

Assembly of the eastern North American herpetofauna: new evidence from lizards and frogs

Darwin first recognized the importance of episodic intercontinental dispersal in the establishment of worldwide biotic diversity. Faunal exchange across the Bering Land Bridge is a major example of such dispersal. Here, we demonstrate with mitochondrial DNA evidence that three independent dispersal events from Asia to North America are the source for almost all lizard taxa found in continental eastern North America. Two other dispersal events across Beringia account for observed diversity among North American ranid frogs, one of the most species-rich groups of frogs in eastern North America. The contribution of faunal elements from Asia via dispersal across Beringia is a dominant theme in the historical assembly of the eastern North American herpetofauna.

Mitochondrial DNA evidence of an early Holocene population expansion of threespine sticklebacks from Scotland

In this study, we analyzed the cytochrome b gene in threespine stickleback ( Gasterosteus aculeatus) populations from Scotland. We found evidence of a postglacial population expansion in Scotland and large differences in genetic diversity estimates among populations. Higher levels of genetic diversity are negatively correlated with distance from the ocean. In addition, distance from the ocean and predation risk both explain variation in plate count in Scottish populations. Overall, the mtDNA data support the racemic model of evolution in threespine stickleback.

Description of a new Tityus species (Scorpiones: Buthidae) from Sierra de Portuguesa, western Venezuela, based on morphological and mitochondrial DNA evidence

A new scorpion species, Tityus imei sp. nov., is described, representing the first record of the genus for the southern foothills of Sierra de Portuguesa in the western Venezuelan state of Portuguesa. The species is morphologically related to T. sanarensis, from the state of Lara, and T. boconoensis, from state of Trujillo. Tityus imei sp. nov. can be distinguished by the array of dorsal trichobothria in the pedipalp femur (d3, d4, d5) and by the following combination of female metasomal segment II characters: (i) ventral keels double and parallel up to two thirds of the segment, whereupon they converge into a single keel and separate again in the base; (ii) full, parallel ventral keels, including a well defined central keel in the second half of the segment. A molecular approach was undertaken to estimate the genetic relationship between the new species, T. sanarensis, T. boconoensis, and T. discrepans. Sequencing of a 562 bp-segment encoding sectors M6 to M11 of the cytochrome oxidase subunit I revealed that T. imei sp. nov. diverges from T. sanarensis and T. boconoensis, particularly in the polymorphic sector I4, sharing more overall sequence similarity with the northcentral Venezuelan species, T. discrepans. The new species is of potential medical importance given the presence of venom components whose mass resembles that of scorpion neurotoxins affecting voltage-sensitive sodium channels, as indicated by MALDI-TOF MS analyses.

Molecular identification of pathogenic house dust mites using 12S rRNA sequences

House dust mites are microarthropods implicated in the cause of allergic diseases. Currently, there is no phylogenetic analysis of dust mites based on genomic or mitochondrial DNA (mtDNA) evidence. For the first time, we report evolutionary relationships based on partial mtDNA 12S rRNA sequences among the four dust mite families Pyroglyphidae (Dermatophagoides pteronyssinus), Glycyphagoidea (Glycyphagus privatus), Acaridae (Aleuroglyphus ovatus), and Echimyopodidae (Blomia tropicalis). Thirteen sequence variants were obtained and phylogenetic analysis showed two monophyletic clades composed of two species each. Contrary to current taxonomic classification, the Acaridae clustered in a monophyletic group with the Pyroglyphidae. Considering the current difficulties in identifying these medically important species for the purpose of eradication and treatment, it is significant that sequence data are capable of discriminating between species belonging to different families of dust mites.

Mitochondrial DNA evidence for a genetic distinction of the native red deer of Mesola, northern Italy, from the Alpine populations and the Sardinian subspecies

Native red deer of Mesola Wood, northern Italy, were compared with the Sardinian subspecies and with some populations from the Italian Alps and Austria using the analysis of restriction fragment length polymorphism (RELP) of mitochondrial (mt) DNA segments. The results highlight the existence of four main genetic lineages, and provide evidence for a structuring of populations according to their geographic occurrence. Two mitochondrial lineages, although highly distantly related, are shared between the populations from the centre-eastern Alps of Italy and Austria, while the other two lineages characterize the Sardinian and Mesola red deer, respectively. The exclusive haplotype found in the Mesola population appears as being an offshot of one of the two main Alpine lineages, suggesting a presumed origin of these deer from a panmictic population which dwelt in mid-southern Europe, prior to the fragmentation of populations caused by human activities and manipulations. Considering their distinctiveness in morphologic and genetic traits, as well as their historical background and biogeographical value, these native deer should be regarded as a national conservation priority. The Sardinian red deer is highly divergent from both Mesola and Alpine populations. However, the controversial question of the phylogeographic origin of this subspecies remains unresolved. The utility of RELP analyses of mtDNA segments as a tool to discriminate among red deer populations as well as to develop effective strategies for their conservation and management.

Resurrection of Bohadschia bivittata from B. marmorata (Holothuroidea: Holothuriidae) based on behavioral, morphological, and mitochondrial DNA evidence

Behavior, color, body size, spicules, and mitochondrial DNA were examined in two morphs from the Bohadschia marmorata (Jaeger, 1833) species complex in Micronesia to test whether they are conspecific. This complex consists of eight morphs that have been described as separate species and combined in various ways for over a century. We examined the classic B. marmorata type and the type originally described as the species B. bivittata (Mitsukuri, 1912); B. bivittata was combined with B. marmorata by Panning (1944). Several observations and a phylogenetic analysis led us to conclude that B. marmorata and B. bivittata should return to their status as separate species. First, B. marmorata lives in shallow areas with strong currents, and B. bivittata lives on open sand between corals in deeper water. Second, the coloration of B. bivittata is distinct from B. marmorata, and although specimens collected on Yap Island differed from Mitsukuri's original description of B. bivittata, no specimens were collected with coloration intermediate between B. bivittata and B. marmorata. Third, spicules are more highly branched, perforated, and spiked in B. bivittata than in B. marmorata (and, in our study, spicule complexity did not correlate with body size). Finally, our phylogenetic analysis, based on partial nucleotide sequences of 16s, 12s, and COI mitochondrial genes, resulted in a tree—( Pearsonothuria graeffei ( Bohadschia marmorata) ( B. argus ( B. bivittata)))—which shows that B. marmorata and B. bivittata are not even sister species, with B. bivittata more closely related to B. argus. Support for the clades for each Bohadschia species was strong, but the clade containing B. argus and B. bivittata had weaker support. Color and spicule examinations made of preserved B. marmorata-complex specimens from the Indo-Pacific as well as behavioral observations in the field also support the resurrection of B. bivittata.

A Molecular Supermatrix of the Rabbits and Hares (Leporidae) Allows for the Identification of Five Intercontinental Exchanges During the Miocene

The hares and rabbits belonging to the family Leporidae have a nearly worldwide distribution and approximately 72% of the genera have geographically restricted distributions. Despite several attempts using morphological, cytogenetic, and mitochondrial DNA evidence, a robust phylogeny for the Leporidae remains elusive. To provide phylogenetic resolution within this group, a molecular supermatrix was constructed for 27 taxa representing all 11 leporid genera. Five nuclear (SPTBN1, PRKCI, THY, TG, and MGF) and two mitochondrial (cytochrome b and 12S rRNA) gene fragments were analyzed singly and in combination using parsimony, maximum likelihood, and Bayesian inference. The analysis of each gene fragment separately as well as the combined mtDNA data almost invariably failed to provide strong statistical support for intergeneric relationships. In contrast, the combined nuclear DNA topology based on 3601 characters greatly increased phylogenetic resolution among leporid genera, as was evidenced by the number of topologies in the 95% confidence interval and the number of significantly supported nodes. The final molecular supermatrix contained 5483 genetic characters and analysis thereof consistently recovered the same topology across a range of six arbitrarily chosen model specifications. Twelve unique insertion-deletions were scored and all could be mapped to the tree to provide additional support without introducing any homoplasy. Dispersal-vicariance analyses suggest that the most parsimonious solution explaining the current geographic distribution of the group involves an Asian or North American origin for the Leporids followed by at least nine dispersals and five vicariance events. Of these dispersals, at least three intercontinental exchanges occurred between North America and Asia via the Bering Strait and an additional three independent dispersals into Africa could be identified. A relaxed Bayesian molecular clock applied to the seven loci used in this study indicated that most of the intercontinental exchanges occurred between 14 and 9 million years ago and this period is broadly coincidental with the onset of major Antarctic expansions causing land bridges to be exposed.

Swimming out of Africa: mitochondrial DNA evidence for late Pliocene dispersal of a cichlid from Central Africa to the Levant

The rich Levantine fauna and flora were shaped by millions of years of migration across the region, from Africa to Eurasia and vice versa. Most large-scale processes that led to this diversity have been relatively well studied. However, small-scale processes, and details such as the area of origin of particular groups, and the route and time of dispersal are often not as clear. This is the case with the endemic Levantine representatives of the fish family Cichlidae. In this work we combine genetic, palaeontological and geological data in an attempt to understand the dispersal of the cichlid fish Astatotilapia flaviijosephi (Lortet, 1883) from sub-Saharan Africa to the Levant. A. flaviijosephi is unique among the Levantine cichlids in being the only non-tilapiine. It is also the only haplochromine cichlid to be found out of Africa. A partial sequence of the control region of the mitochondrial DNA was used to determine A. flaviijosephi ’s phylogenetic relationships with other African haplochromines, and to estimate its time of divergence from this group. Combining our findings with palaeontological and geological data, we suggest that A. flaviijosephi separated from the other haplochromines during the middle to late Pliocene (2.5‐3.3 Mya) and probably dispersed from Africa to the Levant via the Nile. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 103‐109.

Phylogeny of the Dragonfly and Damselfly Order Odonata as Inferred by Mitochondrial 12S Ribosomal RNA Sequences

The phylogenetic relationships among members of the Odonates were inferred from mitochondrial DNA 12S ribosomal RNA sequence data. These data show support for a monophyletic Anisoptera suborder, which are consistent with previous phylogenetic work performed on the group. However, the Zygoptera are paraphyletic based on mitochondrial DNA evidence. In particular, the family Lestidae appears more closely related to the Anisoptera then the Zygoptera.

Nuclear and mitochondrial DNA evidence of polyphyly in the avian superfamily Muscicapoidea

Nucleotide sequences of the nuclear c- mos gene and the mitochondrial cytochrome b and ND2 genes were used to assess the monophyly of Sibley and Monroe’s [Distribution and Taxonomy of Birds of the World, Yale University Press, New Haven, 1990] Muscicapoidea superfamily. The relationships and monophyly of major lineages within the superfamily, as well as genera membership in major lineages was also assessed. Analyses suggest that Bombycillidae is not a part of Muscicapoidea, and there is strongly supported evidence to suggest that Turdinae is not part of the Muscicapidae, but is instead sister to a Sturnidae + Cinclidae clade. This clade is in turn sister to Muscicapidae (Muscicapini + Saxicolini). Of the 49 Turdinae and Muscicapidae genera that we included in our analyses, 10 (20%) are shown to be misclassified to subfamily or tribe. Our results place one current Saxicolini genus in Turdinae, two Saxicolini genera in Muscicapini, and five Turdinae and two Muscicapini genera in Saxicolini; these relationships are supported with 100% Bayesian support. Our analyses suggest that c- mos was only marginally useful in resolving these “deep” phylogenetic relationships.

Mitochondrial DNA evidence for admixed origins of central Siberian populations

The Yakuts of northeastern Siberia are a Turkic-speaking population of horse- and cattle-breeders surrounded by Tungusic-speaking reindeer-herders and hunter-gatherers. Archaeological and ethnohistorical data suggest that Yakuts stem from a common ancestral population with the Buryats living near Lake Baikal. To address this hypothesis, we obtained sequences of the first hypervariable segment (HV1) of the mitochondrial DNA control region from Yakuts and Buryats and compared these with sequences from other Eurasian populations. The mtDNA results show that the Buryats have close affinities with both Central Asian Turkic groups and Mongols, while the Yakuts have close affinities with northeastern Siberian, Tungusic-speaking Evenks and south Siberian, Turkic-speaking Tuvans. This different ancestry of the Yakuts and the Tuvans (compared with other Turkic-speaking groups) most likely reflects extensive admixture that occurred between Turkic-speaking steppe groups and Evenks as the former migrated into Siberia. Moreover, the Yakuts are unique among Siberian populations in having a high number of haplotypes shared exclusively with Europeans, suggesting, contrary to the historical record, that occasionally Yakut men took Russian women as wives.

Mitochondrial dysfunction and the role of the non-specialist laboratory.

Each human cell contains at least 1,000 mitochondria, each containing several copies of mitochondrial DNA. This DNA is tiny compared with the nuclear genome, and its structure and products have been fully elucidated. Whilst oxidative phosphorylation depends on the polypeptides encoded by mitochondrial DNA, it also requires a huge number of nuclear DNA products. Inherited deleterious mutations of mitochondrial DNA leading to inefficient oxidative phosphorylation have been described as 'mitochondrial disorders', with a variety of clinical presentations. When similar clinical presentations occur with no discernible mutation of mitochondrial DNA, histological and biochemical evidence is required for diagnosis. The number of these laboratory-proven inherited mitochondrial disorders is growing. It is also becoming clear that mitochondrial DNA defects can be acquired, the most common cause being therapy with highly active antiretroviral therapy (HAART) for human immunodeficiency virus-1 (HIV-1) infection. Whilst definitive diagnosis of inherited or acquired mitochrondrial dysfunction requires access to specialist laboratory techniques, routine laboratories have a role to play in the initial investigation and monitoring of these conditions.

Prehistoric introduction of domestic pigs onto the Okinawa Islands: ancient mitochondrial DNA evidence.

Ancient DNAs of Sus scrofa specimens excavated from archaeological sites on the Okinawa islands were examined to clarify the genetic relationships among prehistoric Sus scrofa, modern wild boars and domestic pigs inhabiting the Ryukyu archipelago, the Japanese islands, and the Asian continent. We extracted remain DNA from 161 bone specimens excavated from 12 archaeological sites on the Okinawa islands and successfully amplified mitochondrial DNA control region fragments from 33 of 161 specimens. Pairwise difference between prehistoric and modern S. scrofa nucleotide sequences showed that haplotypes of the East Asian domestic pig lineage were found from archaeological specimens together with Ryukyu wild boars native to the Ryukyu archipelago. Phylogenetic analysis of 14 ancient sequences (11 haplotypes; 574 bp) indicated that S. scrofa specimens from two Yayoi-Heian sites (Kitahara and Ara shellmiddens) and two Recent Times sites (Wakuta Kiln and Kiyuna sites) are grouped with modern East Asian domestic pigs. Sus scrofa specimens from Shimizu shellmidden (Yayoi-Heian Period) were very closely related to modern Sus scrofa riukiuanus but had a unique nucleotide insertion, indicating that the population is genetically distinct from the lineage of modern Ryukyu wild boars. This genetic evidence suggests that domestic pigs from the Asian continent were introduced to the Okinawa islands in the early Yayoi-Heian period (1700-2000 BP), or earlier.

A hybrid zone between hydrothermal vent mussels (Bivalvia: Mytilidae) from the Mid-Atlantic Ridge.

This study provides the first example of a hybrid zone between animal taxa distributed along the mid-ocean ridge system. We examined the distribution and genetic structure of deep-sea hydrothermal vent mussels (Bivalvia: Mytilidae) along a 2888-km portion of the Mid-Atlantic Ridge between 37 degrees 50' N and 14 degrees 45' N latitude. Mitochondrial DNA (mtDNA), allozymes and multivariate-morphometric evidence discriminated between individuals of a northern species, Bathymodiolus azoricus, and a southern species, B. puteoserpentis, that were separated by an intermediate ridge segment almost devoid of mussels. A small sample of mussels from Broken Spur, a vent locality along this intermediate zone, revealed a mixed population with gene frequencies and morphology that were broadly intermediate to those of the northern and southern species. Multilocus clines in mtDNA and allozyme frequencies were centred over the intermediate zone. We consider intrinsic and extrinsic processes that might limit genetic exchange across this hybrid zone.

Higher-Level Phylogeny of New World Vireos (Aves: Vireonidae) Based on Sequences of Multiple Mitochondrial DNA Genes

Interfamilial relationships of the New World songbird family Vireonidae are uncertain. Thus, we sequenced 3069 bp of four mitochondrial genes (cyt b, ND2, ND3, COI) from 19 taxa in five families and two outgroups, to examine higher-level alliances with proposed relatives. We also sequenced cyt b and ND2 from an additional five vireonids to examine intergeneric relationships within the Vireonidae and incorporated 14 sequences of cyt b from GenBank to test the effects of taxon sampling on gene tree resolution. Families appeared monophyletic in all analyses, and the affinity of vireonids to Old World corvoids was corroborated. However, relationships among the Vireonidae and other families were not resolved. Sequences of vireonids revealed high levels of divergence within and between genera, with either Cyclarhis or Vireolanius positioned basally, depending on the analysis. On the basis of mitochondrial DNA and biogeographic evidence, vireonids represent a deep lineage derived from an Old World ancestor that colonized the New World, most likely via Beringia, with subsequent radiation in the Middle American tropics. We hypothesize postcolonization dispersal of the ancestor into Middle America, followed by extinction of the ancestor in North America. This extinction event left the North Temperate Zone unoccupied by any vireonid until northward reinvasion by some species of Vireo. Although the closest living relative of vireonids remains unidentified, broad-scale sequencing of additional extant corvoids with multiple molecular markers should further elucidate Old World alliances.

Ancient mitochondrial DNA evidence for prehistoric population movement: the Numic expansion.

The mitochondrial DNA of modern Native Americans has been shown to fall into one of at least five haplogroups (A, B, C, D, or X) whose frequencies differ among tribal groups. The frequencies of these five haplogroups in a collection of ancient individuals from Western Nevada dating to between approximately 350-9,200 years BP were determined. These data were used to test the hypothesis, supported by archaeological and linguistic data, that the current inhabitants of the Great Basin, the Numic speakers, are recent immigrants into the area who replaced the previous non-Numic inhabitants. The frequency distributions of haplogroups in the ancient and modern Native Americans differed significantly, suggesting that there is a genetic discontinuity between the ancient inhabitants and the modern Numic speakers, providing further support for the Recent Numic Expansion hypothesis. The distribution of mitochondrial haplogroups of the ancient inhabitants of the Great Basin is most similar to those of some of the modern Native American inhabitants of California.

Microsatellite diversity and conservation of a relic trout population: McCloud River redband trout.

Rainbow trout native to the McCloud River, California, USA (Oncorhynchus mykiss stonei) are thought to represent a relic, nonanadromous trout adapted to harsh, fragmented environments. These fish, commonly named McCloud River 'redband' trout, survive in their most primitive form in a small, spring-fed stream, Sheepheaven Creek, in the upper McCloud River drainage. Turn-of-the-century fisheries records document both coastal anadromous steelhead and freshwater resident trout within the McCloud River drainage. The phylogenetic position of the McCloud River redband trout within O. mykiss has been debated for over 50 years. Based on phenotypic evidence, these fish were first reported as 'southern Sierra golden trout' by Wales in 1939. Behnke (1970) considered them a relic subspecies of nonanadromous, fine-scaled trout. Allozyme and mitochondrial DNA evidence suggested a coastal lineage. In this study, we examined within- and among-basin genetic associations for Sheepheaven Creek redband trout using 11 microsatellite loci. Within-basin analyses supported unique genetic characteristics in Sheepheaven Creek's trout in comparisons with other McCloud River rainbow trout. Microsatellite data supported significant independence between Sheepheaven Creek fish and hatchery rainbow trout. Inter-basin genetic distance analyses positioned Sheepheaven Creek fish with samples collected from Lassen Creek, a geographically proximate stream containing inland redband trout. California's redband trout shared a close genetic association with Little Kern River golden trout (O.m. whitei) and isolated rainbow trout from Rio Santo Domingo, Baja, Mexico (O.m. nelsoni), suggesting a vicariant distribution of microsatellite diversity throughout the southern range of this species.