Mitochondrial DNA Evidence Research Articles

Migration of a humpback whale (Megaptera novaeangliae) between the Cape Verde Islands and Iceland

The movements of individual humpback whales (Megaptera novaeangliae) can be tracked by matching photographs of the distinctive markings on the ventral sides of their tail flukes. During the winter-spring seasons of 1990, 1991, 1995, 1996, 1999, 2000, 2001 and 2002 a total of 42 individual humpbacks were identified by fluke photographs from the waters of the Cape Verde Islands. These were compared with photographs taken elsewhere in the North Atlantic. One match was made with a whale previously photographed in the Denmark Strait off Iceland, providing the first direct evidence of a link between the humpbacks in tropical waters of the eastern North Atlantic and a high-latitude feeding ground. This finding is consistent with the mitochondrial DNA evidence of at least two distinct breeding populations of humpback whales in the North Atlantic. The presence of cows with young calves as well as singers during the humpback mating and calving season implies that waters surrounding the Cape Verde archipelago constitute a breeding and calving ground for an eastern North Atlantic population of humpback whales.

Impact of in-depth information and multimedia presentation on mock jurors’ comprehension of mitochondrial DNA evidence

In the courtroom, jurors are often faced with the task of evaluating complex scientific evidence. However, research suggests that jurors' understanding of complex scientific evidence and its reliability can be prone to error. Therefore, it is important to explore how jurors' comprehension of such evidence can be improved. The present study examined mock jurors' (N = 162) understanding of mitochondrial DNA (mtDNA) and its reliability using a 3 (evidence presentation: basic information vs. in-depth information vs. multimedia information) x 2 (evidence strength: stronger vs. weaker) factorial design. The basic information condition was kept short and served as a baseline measure of participants' knowledge on the subject. Participants read an expert witness testimony about mtDNA evidence in a robbery case and then answered 18 true/false questions to assess their understanding of the mtDNA evidence and its reliability. The strength of evidence did not have a statistically significant effect on jurors' understanding of the evidence or its reliability, and no interaction effects were observed. For the presentation of evidence, by contrast, providing in-depth information on mtDNA evidence significantly improved mock jurors' understanding of both the mtDNA evidence and its reliability. Additional illustrations presented together with the in-depth information did not further improve jurors' scores, although exploratory post-hoc analyses suggested that the multimedia information may have facilitated jurors’ understanding of some aspects of the mtDNA evidence. Theoretical and practical implications of the findings are discussed.

Phenotypic variation and polymorphism confirmed among white-bellied swiftlets of the Collocalia esculenta group (Apodidae, Collocaliini) by mitochondrial and nuclear DNA evidence

Among white-bellied glossy swiftlets of the Collocalia group, A. R. Wallace was first to recognise the Makassar Strait, separating Borneo and Sulawesi, as a geographical barrier between different phenotypes: plain-tailed to the west and spot-tailed to the east. Other morphological characters used to define species within the group have been blue or green gloss to the dorsal plumage, and the presence or absence of a single minute tufted feather on the hallux. The value of these characters as taxonomic markers is now known to be unreliable due to the discovery of phenotypically mixed populations east of the Makassar Strait, from North Maluku province, I ndonesia, through Papua New Guinea to New Ireland. We combine field observations of plumage characters with genetic evidence to establish taxonomy of Collocalia group swiftlets. Sequencing specific mitochondrial genes (Cytb and ND2), the nuclear-encoded Fib gene, and a subset of mitochondrial genomes provided data for phylogenetic analysis. Genetic divergence of c.4.7% is observed between two Collocalia clades either side of the Makassar Strait: the plain-tailed C. affinis cyanoptila sampled at Fraser's Hill, Peninsular Malaysia, and a phenotypically mixed population of C. esculenta spilura from North Maluku, Indonesia. Each population formed high-affinity genetic clades, within which divergence was <0.5%. These findings are consistent with geographic but not phenotypic separation between populations. We therefore conclude taxonomy based on these plumage features in glossy swiftlets of the Collocaliini is unreliable.

Genetic evidence further elucidates the history and extent of badger introductions from Great Britain into Ireland.

The colonization of Ireland by mammals has been the subject of extensive study using genetic methods and forms a central problem in understanding the phylogeography of European mammals after the Last Glacial Maximum. Ireland exhibits a depauperate mammal fauna relative to Great Britain and continental Europe, and a range of natural and anthropogenic processes have given rise to its modern fauna. Previous Europe-wide surveys of the European badger (Meles meles) have found conflicting microsatellite and mitochondrial DNA evidence in Irish populations, suggesting Irish badgers have arisen from admixture between human imported British and Scandinavian animals. The extent and history of contact between British and Irish badger populations remains unclear. We use comprehensive genetic data from Great Britain and Ireland to demonstrate that badgers in Ireland's northeastern and southeastern counties are genetically similar to contemporary British populations. Simulation analyses suggest this admixed population arose in Ireland 600–700 (CI 100–2600) years before present most likely through introduction of British badgers by people. These findings add to our knowledge of the complex colonization history of Ireland by mammals and the central role of humans in facilitating it.

Palaeoproteomics resolves sloth relationships.

The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in combination with published mitochondrial DNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America.

The genus Mercuria Boeters, 1971 in Morocco: first molecular phylogeny of the genus and description of two new species (Caenogastropoda, Truncatelloidea, Hydrobiidae)

The western Palearctic freshwater snail genus Mercuria (Caenogastropoda: Hydrobiidae) comprises 26 species primarily distributed in lowland localities of Western Europe and North Africa. Although this genus in North Africa has received considerable attention in terms of species discoveries through morphological descriptions, its distribution and phylogenetic patterns remain unknown. Based on morphological and mitochondrial DNA (mtCOI) evidence, this study examines the three Mercuria species (M.bakeri, M.tingitana, and M.targouasensis) from Morocco identified so far. Besides expanding on information regarding the anatomy of these species, two new species (M.midarensissp. n. and M.tensiftensissp. n.) are described for this region and phylogenetic relationships inferred between these species and the European M.emiliana and M.similis. All Moroccan and European species were recovered as independent entities according to these phylogenetic inferences (uncorrected p-distances 2.8–8.5%) and DNA barcode data. Moroccan Mercuria species clustered with M.emiliana from Spain, although basal relationships within this clade were not well supported. Given that factors such as the season when specimens are collected, habitat type, and parasites could be responsible for the remarkable intraspecific variation observed in shell and penis morphology, it is proposed that the most efficient approach to delimit and identify Mercuria species is to combine morphological descriptions with genetic data.

The genus Mercuria Boeters, 1971 in Morocco: first molecular phylogeny of the genus and description of two new species (Caenogastropoda, Truncatelloidea, Hydrobiidae).

The western Palearctic freshwater snail genus Mercuria (Caenogastropoda: Hydrobiidae) comprises 26 species primarily distributed in lowland localities of Western Europe and North Africa. Although this genus in North Africa has received considerable attention in terms of species discoveries through morphological descriptions, its distribution and phylogenetic patterns remain unknown. Based on morphological and mitochondrial DNA (mtCOI) evidence, this study examines the three Mercuria species (M.bakeri, M.tingitana, and M.targouasensis) from Morocco identified so far. Besides expanding on information regarding the anatomy of these species, two new species (M.midarensissp. n. and M.tensiftensissp. n.) are described for this region and phylogenetic relationships inferred between these species and the European M.emiliana and M.similis. All Moroccan and European species were recovered as independent entities according to these phylogenetic inferences (uncorrected p-distances 2.8–8.5%) and DNA barcode data. Moroccan Mercuria species clustered with M.emiliana from Spain, although basal relationships within this clade were not well supported. Given that factors such as the season when specimens are collected, habitat type, and parasites could be responsible for the remarkable intraspecific variation observed in shell and penis morphology, it is proposed that the most efficient approach to delimit and identify Mercuria species is to combine morphological descriptions with genetic data.

According to mitochondrial DNA evidence, Parascaris equorum and Parascaris univalens may represent the same species.

Parascarosis is caused mainly by parasitic infections with Parascaris equorum and Parascaris univalens, the most common ascarid nematodes, in the small intestine of equines. Parascarosis often causes severe illness and even death in foals and yearlings. In this study, we obtained the complete sequence of the P. equorum mitochondrial (mt) genome and compared its organization and structure with that of P. equorum Japan isolate (nearly complete), and the complete mtDNA sequences of P. univalens Switzerland and USA isolates. The complete mtDNA genome of P. equorum China isolate is 13,899 base pairs (bp), making it the smallest of the four genomes. All four Parascaris mt genomes are circular, and all genes are transcribed in the same direction. The P. equorum mtDNA genome consists of 12 protein-coding genes, two ribosomal RNA genes, 22 transfer (t) RNA genes and one non-coding region, which is consistent with P. equorum Japan isolate and P. univalens Switzerland isolate but distinct from P. univalens USA isolate, which has 20 tRNA genes. Differences in nucleotide sequences of the four entire mt genomes range from 0.1-0.9%, and differences in total amino acid sequences of protein-coding genes are 0.2-2.1%. Phylogenetic analyses showed that the four Parascaris species clustered in a clade, indicating that P. equorum and P. univalens are very closely related. These mt genome datasets provide genetic evidence that P. equorum and P. univalens may represent the same species, which will be of use in further studies of the taxonomy, systematics and population genetics of ascarids and other nematodes.

The virome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals the first report of DNA fragments corresponding to replicating non-retroviral RNA viruses in fungi.

Arbuscular Mycorrhizal Fungi (AMF) are key components of the plant microbiota. AMF genetic complexity is increased by the presence of endobacteria, which live inside many species. A further component of such complexity is the virome associated to AMF, whose knowledge is still very limited. Here, by exploiting transcriptomic data we describe the virome of Gigaspora margarita. A BLAST search for viral RNA-dependent RNA polymerases sequences allowed the identification of four mitoviruses, one Ourmia-like narnavirus, one Giardia-like virus, and two sequences related to Fusarium graminearum mycoviruses. Northern blot and RT-PCR confirmed the authenticity of all the sequences with the exception of the F. graminearum-related ones. All the mitoviruses are replicative and functional since both positive strand and negative strand RNA are present. The abundance of the viral RNA molecules is not regulated by the presence or absence of Candidatus Glomeribacter gigasporarum, the endobacterium hosted by G. margarita, with the exception of the Ourmia-like sequence which is absent in bacteria-cured spores. In addition, we report, for the first time, DNA fragments corresponding to mitovirus sequences associated to the presence of viral RNA. These sequences are not integrated in the mitochondrial DNA and preliminary evidence seems to exclude integration in the nuclear genome.

ミトコンドリアDNA および核DNA の解析による魚取沼テツギョの起源

ミトコンドリアDNA および核DNA の解析による魚取沼テツギョの起源

Mitochondrial DNA Evidence Supports the Hypothesis that Triodontophorus Species Belong to Cyathostominae.

Equine strongyles, the significant nematode pathogens of horses, are characterized by high quantities and species abundance, but classification of this group of parasitic nematodes is debated. Mitochondrial (mt) genome DNA data are often used to address classification controversies. Thus, the objectives of this study were to determine the complete mt genomes of three Cyathostominae nematode species (Cyathostomum catinatum, Cylicostephanus minutus, and Poteriostomum imparidentatum) of horses and reconstruct the phylogenetic relationship of Strongylidae with other nematodes in Strongyloidea to test the hypothesis that Triodontophorus spp. belong to Cyathostominae using the mt genomes. The mt genomes of Cy. catinatum, Cs. minutus, and P. imparidentatum were 13,838, 13,826, and 13,817 bp in length, respectively. Complete mt nucleotide sequence comparison of all Strongylidae nematodes revealed that sequence identity ranged from 77.8 to 91.6%. The mt genome sequences of Triodontophorus species had relatively high identity with Cyathostominae nematodes, rather than Strongylus species of the same subfamily (Strongylinae). Comparative analyses of mt genome organization for Strongyloidea nematodes sequenced to date revealed that members of this superfamily possess identical gene arrangements. Phylogenetic analyses using mtDNA data indicated that the Triodontophorus species clustered with Cyathostominae species instead of Strongylus species. The present study first determined the complete mt genome sequences of Cy. catinatum, Cs. minutus, and P. imparidentatum, which will provide novel genetic markers for further studies of Strongylidae taxonomy, population genetics, and systematics. Importantly, sequence comparison and phylogenetic analyses based on mtDNA sequences supported the hypothesis that Triodontophorus belongs to Cyathostominae.

Two new species of Fluminicola (Caenogastropoda, Lithoglyphidae) from southwest Oregon, USA, and a range extension for F. multifarius

We describe two new species of pebblesnails (Lithoglyphidae: Fluminicola) from southwest Oregon based on morphologic and mitochondrial DNA (COI, cytB) evidence. Fluminicola umpquaensis sp. n., which had been traditionally identified as F. virens prior to the recent restriction of the latter to the lower Columbia River drainage, lives in lotic habitats in the Umpqua River basin. This species is readily distinguished from closely related F. gustafsoni and F. virens by shell and anatomical characters, and by its mtDNA sequences (divergence >3.6% for both genes). Fluminicola fresti sp. n. ranges among lotic habitats in the North Umpqua River basin, and in the upper Rogue River drainage north of Little Butte Creek. This species differs from other congeners by >9.1% for both genes and is distinguished from closely similar and geographically proximal F. multifarius by several anatomical characters. Additionally, new records are provided for F. multifarius from the upper Rogue River basin south of Little Butte Creek, which extend the geographic range of this species about 80 km northward from the Sacramento River headwater region. This continues a recent series of taxonomic papers on the poorly known and little studied pebblesnail fauna of the vast Pacific watershed from northern California to southern British Columbia.

Mitochondrial DNA Evidence Reveals Genetic Difference between Perny's Long-Nosed Squirrels in Taiwan and Asian Mainland

Abstract. Taiwan Island is thought to have formed around 6.0 million years ago, but, the formation of a ‘proto-Taiwan’ began around 9.0 million years ago. During the late Miocene, the proto-Taiwan is thought to have been a part of the Asian mainland. During the Pleistocene, Taiwan Island was again occasionally connected with the Asian mainland. Several mammal species migrated from the Asian mainland to Taiwan during Pleistocene glacial periods. Despite the connections between Taiwan and the Asian mainland, Taiwan has some endemic mammal species. Recent genetic evidence suggests that arboreal squirrels (Petaurista alborufus, P. philippensis, Belomys pearsonii, and Tamiops maritimus) adapted to Taiwan's mountainous forests are endemic species. Since these squirrels may have similarly evolved from separate ancestral stock in Taiwan, we investigated the phylogenetic relationship of Perny's long-nosed squirrel (Dremomys pernyi) from Taiwan and the Asian mainland by using mitochondrial cytochrome b gene sequenc...

Application of a mitochondrial DNA control region frequency database for UK domestic cats

DNA variation in 402bp of the mitochondrial control region flanked by repeat sequences RS2 and RS3 was evaluated by Sanger sequencing in 152 English domestic cats, in order to determine the significance of matching DNA sequences between hairs found with a victim’s body and the suspect’s pet cat. Whilst 95% of English cats possessed one of the twelve globally widespread mitotypes, four new variants were observed, the most common of which (2% frequency) was shared with the evidential samples. No significant difference in mitotype frequency was seen between 32 individuals from the locality of the crime and 120 additional cats from the rest of England, suggesting a lack of local population structure. However, significant differences were observed in comparison with frequencies in other countries, including the closely neighbouring Netherlands, highlighting the importance of appropriate genetic databases when determining the evidential significance of mitochondrial DNA evidence.

Separation of a novel species from Actinopyga mauritiana (Holothuroidea: Holothuriidae) species complex, based on ecological, morphological and mitochondrial DNA evidence.

Separation of a novel species from Actinopyga mauritiana (Holothuroidea: Holothuriidae) species complex, based on ecological, morphological and mitochondrial DNA evidence.

Nesting by Canada Geese on Baffin Island, Nunavut

Outside of northern Quebec, there is little evidence to confirm reports of nesting by Canada Geese in Arctic habitats of North America, but they nest regularly in the Arctic tundra of West Greenland, from about 62˚ N to as far north as 76.96˚ N, 71.11˚ W. In 2013, we documented successful nesting by a pair of Canada Geese on northern Baffin Island (71.36˚ N, 79.59˚ W), approximately 1200 km north of the nearest known site of regular nesting by this species in northern Quebec. Photographs, egg measurements, and mitochondrial DNA evidence confirmed that these were Canada Geese. Egg laying began around 17 June, the nest of five eggs hatched on 18 July, and we determined that fledging should have occurred around 20 September. Daily mean temperatures on northern Baffin Island fell below freezing after 5 September 2013, and we suspect that the probability of recruitment for this brood was very low. Climate warming in the Arctic is likely to favor northward range expansion by Canada Geese.

Geographical ancestry of Lake Malawi's cichlid fish diversity.

The Lake Malawi haplochromine cichlid flock is one of the largest vertebrate adaptive radiations. The geographical source of the radiation has been assumed to be rivers to the south and east of Lake Malawi, where extant representatives of the flock are now present. Here, we provide mitochondrial DNA evidence suggesting the sister taxon to the Lake Malawi radiation is within the Great Ruaha river in Tanzania, north of Lake Malawi. Estimates of the time of divergence between the Lake Malawi flock and this riverine sister taxon range from 2.13 to 6.76 Ma, prior to origins of the current radiation 1.20-4.06 Ma. These results are congruent with evaluations of 2-3.75 Ma fossil material that suggest past faunal connections between Lake Malawi and the Ruaha. We propose that ancestors of the Malawi radiation became isolated within the catchment during Pliocene rifting that formed both Lake Malawi and the Kipengere/Livingstone mountain range, before colonizing rivers to the south and east of the lake region and radiating within the lake basin. Identification of this sister taxon allows tests of whether standing genetic diversity has predisposed Lake Malawi cichlids to rapid speciation and adaptive radiation.

A new species of the Miniopterus schreibersii species complex (Chiroptera: Miniopteridae) from the Maghreb Region, North Africa

We used an integrative approach combining cranio-dental characters, mitochondrial and nuclear data and acoustic data to show the presence in the genus Miniopterus of a cryptic species from the Maghreb region. This species was previously recognised as Miniopterus schreibersii (Kuhl, 1817). Miniopterus maghrebensis sp. nov. can be differentiated from M. schreibersii sensu stricto on the basis of cranial characters and from mitochondrial DNA and microsatellite evidence. Although slight external morphological and acoustic differences were noted between the two species, these criteria alone did not allow reliable species identification from live animals. Based on the specimens identified morphologically and/or genetically, the distribution range of M. maghrebensis sp. nov. extends from northern Morocco to south of the High Atlas Mountains and northern Tunisia. The new cryptic species is found in sympatry with M. schreibersii s.str. near coastal regions of North Africa.

Mitochondrial DNA and microsatellite markers evidence a different pattern of hybridization in red-legged partridge (Alectoris rufa) populations from NW Italy

Genetic introgression with exotic genomes represents a major conservation concern for the red-legged partridge (Alectoris rufa, Phasianidae). In particular, massive releases of chukar partridges (Alectoris chukar) and/or red-legged × chukar partridge hybrids for hunting purposes have cast serious doubts on the Italian present-day occurrence of wild A. rufa populations not affected by introgressive hybridization. This study investigates the genetic structure of red-legged partridges populations in two ecologically different areas in Northern Italy. Analysis of maternal mitochondrial DNA and biparental microsatellite markers excluded the presence of hybridization in a typical agricultural habitat where hunting and release of reared birds are strictly banned. By contrast, signs of chukar introgression were detected in a perifluvial habitat unusual for the red-legged partridge in Italy. The present study documents the first red-legged partridge population with no genetic evidences of recent chukar introgression presently living in Italy. We recommend that urgent conservation actions are taken to preserve the genetic integrity of this population from the risk of hybridization with farm-reared birds and to support its long-term conservation.

Mitochondrial DNA Evidence Indicates the Local Origin of Domestic Pigs in the Upstream Region of the Yangtze River

Previous studies have indicated two main domestic pig dispersal routes in East Asia: one is from the Mekong region, through the upstream region of the Yangtze River (URYZ) to the middle and upstream regions of the Yellow River, the other is from the middle and downstream regions of the Yangtze River to the downstream region of the Yellow River, and then to northeast China. The URYZ was regarded as a passageway of the former dispersal route; however, this assumption remains to be further investigated. We therefore analyzed the hypervariable segements of mitochondrial DNA from 513 individual pigs mainly from Sichuan and the Tibet highlands and 1,394 publicly available sequences from domestic pigs and wild boars across Asia. From the phylogenetic tree, most of the samples fell into a mixed group that was difficult to distinguish by breed or geography. The total network analysis showed that the URYZ pigs possessed a dominant position in haplogroup A and domestic pigs shared the same core haplotype with the local wild boars, suggesting that pigs in group A were most likely derived from the URYZ pool. In addition, a region-wise network analysis determined that URYZ contains 42 haplotypes of which 22 are unique indicating the high diversity in this region. In conclusion, our findings confirmed that pigs from the URYZ were domesticated in situ.