An empirical test of freshwater vicariance via river capture

River capture is a geomorphological process through which stream sections are displaced from one catchment to another, and it may represent a dominant facilitator of interdrainage transfer and cladogenesis in freshwater-limited taxa. However, few studies have been conducted in a manner to explicitly test the biological significance of river capture. Here we present a multispecies phylogeographical analysis to test whether the nonmigratory fish fauna of the Von River (South Island, New Zealand) is the product of a well-documented, Late Quaternary capture of a section of the Oreti River (Southland drainage). Specifically, we predict that nonmigratory fishes of the Von River will exhibit closer genetic affinities with those of Southland, rather than those of the Clutha system, into which the Von River presently drains. Mitochondrial DNA phylogeography (control region and cytochrome b sequence data) and analysis of nuclear orthologues of mtDNA sequences indicate that 'flathead'Galaxias of the Von River (n = 31, three sites) have greatest genetic affinities with those of Southland (Galaxias 'southern', n = 216, 38 sites), rather than with those of the Clutha River (Galaxias sp. 'D', n = 73, 32 sites). Likewise, Von River 'roundhead'Galaxias (n = 52, four sites) have greatest genetic affinities with those of Southland drainages (Galaxias gollumoides, n = 223, 58 sites), rather than with those of the Clutha River (Galaxias pullus, Galaxias anomalus, Galaxias gollumoides of the Nevis tributary; n = 68, 32 sites). These findings are consistent with our predictions that genetic affinities of the nonmigratory fish fauna in the Von River would reflect past, rather than present, drainage connections. Consequently, river capture is responsible for the nonmigratory fish fauna of the Von River. In a broader context, river capture has frequently influenced the distribution of genetic lineages among catchments in New Zealand freshwater-limited fish, and its biogeographical significance may have been underestimated in other regions.     

Mitochondrial DNA variation in Spanish populations of Ceratitis capitata (Wiedemann) (Tephritidae) and the colonization process

Abstract: Mitochondrial DNA variation in the Mediterranean fruit fly Ceratitis capitata (Wiedemann, Diptera: Tephritidae) was studied in three natural populations from southern, central and eastern Spain by means of restriction fragment length polymorphisms using 22 restriction endonucleases. Nine different haplotypes were found based upon the restriction patterns of the seven polymorphic endonucleases, providing a measure of discrimination between populations (N_ST = 0.2462, F_ST = 0.154). The observed distribution of haplotypes, corroborated by a parsimonious unrooted tree, suggests an ancient origin for haplotype VII, and a first step in the colonization of the Iberian Peninsula and subsequently the northern and eastern Mediterranean basin, through the Straits of Gibraltar. No relationship can be established between the colonization process for Europe and America.     

Mitochondrial DNA analyses of Indian water buffalo support a distinct genetic origin of river and swamp buffalo

Water buffalo (Bubalus bubalis) is broadly classified into river and swamp categories, but it remains disputed whether these two types were independently domesticated, or if they are the result of a single domestication event. In this study, we sequenced the mitochondrial D-loop region and cytochrome b gene of 217 and 80 buffalo respectively from eight breeds/locations in northern, north-western, central and southern India and compared our results with published Mediterranean and swamp buffalo sequences. Using these data, river and swamp buffalo were distinguished into two distinct clades. Based upon the existing knowledge of cytogenetic, ecological and phenotypic parameters, molecular data and present-day distribution of the river and swamp buffalo, we suggest that these two types were domesticated independently, and that classification of the river and swamp buffalo as two related subspecies is more appropriate.     

Mitochondrial DNA variation in North American Oedipodinae

Restriction fragment analysis of mitochondrial DNA (mtDNA) was used to examine genetic variation and population structure in 13 species of banded-winged grasshoppers (subfamily Oedipodinae). Total DNA of 246 individuals was digested with 11 restriction enzymes and probed with three clonedEcoRI fragments representing the entire mitochondrial genome ofMelanoplus sanguinipes. On average, members of this subfamily were five times more variable than those in another subfamily, Melanoplinae, previously examined. This would appear to lend support to Vickery's claim that the time of origin of Nearctic oedipodines is more ancient than that of melanoplines. With respect to population structure, a few different patterns were exhibited. Species such asCamnula pellucida had populations containing a mixture of haplotypes, some widespread and some geographically restricted. In contrast,Chortophaga viridifasciata populations were characterized by unique assemblages of diverse haplotypes. Phylogeographic hypotheses are advanced to account for these observations.     

Mitochondrial DNA variation in the Viking age population of Norway

The medieval Norsemen or Vikings had an important biological and cultural impact on many parts of Europe through raids, colonization and trade, from about AD 793 to 1066. To help understand the genetic affinities of the ancient Norsemen, and their genetic contribution to the gene pool of other Europeans, we analysed DNA markers in Late Iron Age skeletal remains from Norway. DNA was extracted from 80 individuals, and mitochondrial DNA polymorphisms were detected by next-generation sequencing. The sequences of 45 ancient Norwegians were verified as genuine through the identification of damage patterns characteristic of ancient DNA. The ancient Norwegians were genetically similar to previously analysed ancient Icelanders, and to present-day Shetland and Orkney Islanders, Norwegians, Swedes, Scots, English, German and French. The Viking Age population had higher frequencies of K*, U*, V* and I* haplogroups than their modern counterparts, but a lower proportion of T* and H* haplogroups. Three individuals carried haplotypes that are rare in Norway today (U5b1b1, Hg A* and an uncommon variant of H*). Our combined analyses indicate that Norse women were important agents in the overseas expansion and settlement of the Vikings, and that women from the Orkneys and Western Isles contributed to the colonization of Iceland.     

Mitochondrial DNA variation and population genetic structure of the northern redbelly dace (Phoxinus eos)

Two sections of the control region and the genes coding for NADH dehydrogenase sub-units 5 and 6 (ND-5/6) of mitochondrial DNA (mtDNA) were amplified from Phoxinus eos with the polymerase chain reaction. Both sections of the control region were sequenced directly while the ND-5/6 fragment was sequenced in from each end only. Additionally, the entire ND-5/6 fragment was examined for sequence variation using RFLP analysis. No sequence variation was detected in the control region among 70 individuals sampled from 18 populations across three Ontario regions (Spanish River, Madawaska R. and Cataraqui R.). To examine ND-5/6 variation, a total of 75 individuals were sampled from five populations representing two of the three regions (Madawaska River and Cataraqui R.). Six haplotypes were detected by direct sequencing and four by RFLP analysis. Estimates of population subdivision from RFLP data, sequence analysis, and the two data sets combined for the ND-5/6 fragment, suggest that gene flow is restricted within and between regions. However, estimates of sequence divergence for both sequence and RFLP analysis of this fragment suggested that populations were either founded by already differentiated populations or that populations were founded by a single stock and divergence between regions occurred prior to isolation of populations within regions. These estimates of population structure are much greater than those obtained from allozyme analysis. Additionally, high levels of heterozygosity in nuclear DNA, but low mtDNA diversity suggests that populations have experienced reductions in population size sufficient to reduce only mtDNA variation. Random lineage extinction and limited time for the accumulation of new mutations are likely responsible for low levels of mtDNA variation in ND-5/6 and the control region, while functional constraints may limit variation more than expected in the control region in dace and other fishes.     

Mitochondrial DNA variation in Atlantic capelin, Mallotus villosus: a comparison of restriction and sequence analyses

Divergence estimates were calculated using restriction analysis and cytochrome-b sequences for capelin Mallotus villosus mitochondrial genomes sampled from Newfoundland and Norwegian populations. On average, pairwise divergence values based on cytochrome-b sequences were 2.7 times greater than those based on restriction data. Since the rate of evolution in the cytochrome-b gene is low, it appears that restriction analysis underestimated divergence values, possibly due to limited sensitivity of this method when variable nucleotide positions are not randomly distributed. Mitochondrial genotypes were not shared among the two populations.     

Mitochondrial DNA sequence variation and phylogeography among Salmo trutta L. (Greek brown trout) populations

To investigate the phylogenetic relationships and geographical structure among brown trout S. trutta L. populations from the South Adriatic-Ionian and Aegean sea basins, mitochondrial DNA nucleotide sequence comparisons were used. A 310-base-pair (bp) segment of the control region (D-loop), and an additional 280-bp segment of the cytochrome b gene were sequenced from representatives of 13 brown trout populations. Phylogenetic analyses, conducted after combining the data presented with published data from other Eurasian brown trout, revealed four major phylogenetic groups, three of which were found widely distributed within the southern Balkan region. The phylogeographical patterns revealed by mtDNA represent one of the few cases where phylogenetic discontinuity in a gene tree exists without obvious geographical localization within a species' range and has most likely resulted from the differentiation of the major mtDNA clades during Messinian or early Pleistocene times. Finally, the genetic relationships among the populations suggested by mtDNA were generally not in accordance with either allozyme or morphological data.     

Mitochondrial DNA as a genetic marker for brown trout, Salmo trutta L., populations

Mitochondrial DNA was examined in natural and hatchery-reared stocks of brown trout, using different methods of restriction analysis. The methods included the development of a brown trout mt DNA hybridization probe through cloning part of the brown trout mitochondrial genome. In addition, fragments were analysed by ethidium bromide staining and end-labelling. The relative merits of each of these methods in assessing levels of genetic relatedness between the natural and hatchery-reared brown trout stocks were evaluated. In addition, the study revealed a diagnostic mtDNA restriction pattern which could be used as a genetic marker for the discrimination of these two groups of brown trout.     

Evolution and biogeography of New Zealand's longjaw galaxiids (Osmeriformes: Galaxiidae): the genetic effects of glaciation and mountain building

1. The biological impact of glaciation in Southern Hemisphere freshwaters is poorly understood. Several large rivers of eastern South Island, New Zealand, represent a mosaic of glaciated and non-glaciated regions, and are thus well-suited for studies of post-glacial recolonization.
2. We conducted mtDNA analyses of South Island's endemic non-migratory longjaw galaxiids Galaxias prognathus and G. cobitinis (Osmeriformes: Galaxiidae) to test hypotheses of post-glacial recolonization, and to assess the vicariant effects of Pleistocene mountain building.
3. We analysed the phylogeography of longjaw cytochrome b sequences from 38 sites in central South Island ( n  = 83). On the basis of our sampling it seems that G. prognathus and G. cobitinis have a parapatric distribution in the Waitaki River system, their disjunction broadly coinciding with three large post-glacial lakes. Waitaki clades of both species are deeply divergent relative to conspecific taxa in drainages to the north and south.
4. Tests for recent population growth – predicted under post-glacial expansion of G. prognathus – do not refute recent recolonization of streams above glaciated lakes in the Waitaki River drainage. The apparent absence of potential 'source' populations from non-glaciated regions suggests a post-glacial population decline for G. prognathus below the Waitaki lakes.
5. Molecular clock calibrations based on several freshwater vicariant events elsewhere in New Zealand supported the geologically-derived hypothesis of Waitaki–Canterbury drainage isolation approximately 300 ka.     

Phylogenetic Relationships of the Macaques (Cercopithecidae: Macaca), Inferred from Mitochondrial DNA Sequences

To study the phylogenetic relationships of the macaques, five gene fragments were sequenced from 40 individuals of eight species: Macaca mulatta, M. cyclopis, M. fascicularis, M. arctoides, M. assamensis, M. thibetana, M. silenus, and M. leonina. In addition, sequences of M. sylvanus were obtained from Genbank. A baboon was used as the outgroup. The phylogenetic trees were constructed using maximum-parsimony and Bayesian methods. Because five gene fragments were from the mitochondrial genome and were inherited as a single entity without recombination, we combined the five genes into a single analysis. The parsimony bootstrap proportions we obtained were higher than those from earlier studies based on the combined mtDNA dataset. Excluding M. arctoides, our results are generally consistent with the classification of Delson (1980). Our phylogenetic analyses agree with earlier studies suggesting that the mitochondrial lineages of M. arctoides share a close evolutionary relationship with the mitochondrial lineages of the fascicularis group of macaques (and M. fascicularis, specifically). M. mulatta (with respect to M. cyclopis), M. assamensis assamensis (with respect to M. thibetana), and M. leonina (with respect to M. silenus) are paraphyletic based on our analysis of mitochondrial genes.     

Molecular Characterization of a Mitochondrial DNA Segment from the Japanese Scallop (Patinopecten yessoensis): Demonstration of a Region Showing Sequence Polymorphism in the Population

A 1.3-kb mitochondrial DNA segment from the Japanese scallop Patinopecten yessoensis was cloned and sequenced. This segment contained the transfer RNA^Met gene and partial sequences of 2 ribosomal RNA genes, together with 2 separate noncoding regions (designated NcR1 and NcR2). The NcR regions derived from 78 individuals cultured in Lake Saroma or Matsu Bay, were sequenced, and we found 15 loci with sequence alterations including 13 substitutions, 1 deletion, and 1 insertion (1 locus in NcR1, 14 loci in NcR2), and 17 haplotypes. Of the 17 haplotypes, 10 were found in the Saroma population only, 3 in the Mutsu population only, and 4 in both populations. The gene diversity and nucleotide diversity values were, respectively, 0.87 and 0.0069 for the Saroma population, 0.63 and 0.0040 for the Mutsu population, and 0.83 and 0.0203 overall. Thus the NcR segment was considered to have sufficient sequence variation for population genetic studies. The 16 variants of the NcR2 sequence were separated successfully by denaturing gradient gel electrophoresis, confirming the sequence variation in NcR2. Received October 3, 2001; accepted February 19, 2001.     

Mitochondrial control region and 12S rRNA variation in Przewalski's horse (Equus przewalskii)

Variation in the control region and the 12S rRNA gene of all surviving mitochondrial lineages of Przewalski's horse was investigated. Variation is low despite the present day population being descended from 13 individuals probably representing animals from three different regions of its range. Phylogenetic comparison of these sequences, with sequences for the domestic horse, does not resolve the ancestral status of either horse.     

Mitochondrial DNA (mtDNA) haplogroups in 1526 unrelated individuals from 11 Departments of Colombia

The frequencies of four mitochondrial Native American DNA haplogroups were determined in 1526 unrelated individuals from 11 Departments of Colombia and compared to the frequencies previously obtained for Amerindian and Afro-Colombian populations. Amerindian mtDNA haplogroups ranged from 74% to 97%. The lowest frequencies were found in Departments on the Caribbean coast and in the Pacific region, where the frequency of Afro-Colombians is higher, while the highest mtDNA Amerindian haplogroup frequencies were found in Departments that historically have a strong Amerindian heritage. Interestingly, all four mtDNA haplogroups were found in all Departments, in contrast to the complete absence of haplogroup D and high frequencies of haplogroup A in Amerindian populations in the Caribbean region of Colombia. Our results indicate that all four Native American mtDNA haplogroups were widely distributed in Colombia at the time of the Spanish conquest.     

Onset of cryptic vicariance in the Japanese dormouse Glirulus japonicus (Mammalia, Rodentia) in the Late Tertiary, inferred from mitochondrial and nuclear DNA analysis

The sequences of the mitochondrial cytochrome b gene and restriction site variation in the spacer region of the nuclear ribosomal RNA gene [rDNA-restriction fragment length polymorphism (RFLP)] were analysed to determine the phylogeographic structure of the Japanese dormouse ( Glirulus japonicus ), which is threatened by deforestation and has been designated an endangered species in Japan. The phylogenetic tree of cytochrome b grouped G. japonicus into six geographical populations: north-eastern Honshu (I), central Honshu (II), west-central Honshu/Kii Peninsula (III), western Honshu (IV), Shikoku (V), and westernmost Honshu/Kyushu (VI); the genetic distances among these groups suggest divergence in the Late Tertiary. The lineage of group VI was located at the basal position in the phylogenetic tree, followed by the radiation of the other lineages. An rDNA-RFLP analysis of 15 restriction sites roughly supported such genetic isolation; groups I, II, III, IV, V and VI have five, two, one, one, one and four unique restriction sites, respectively, revealing four geographic groups as cryptic species: I, II, III + IV + V and VI. Our results reveal the ancient divergences of the local population, which has a complicated evolutionary history, and should be useful in developing a framework for the conservation of this species.     

Genetic reconstruction of the population dynamics of a carnivorous marsupial (Antechinus flavipes) in response to floods

Human activities such as regulating river flows, logging and removing fallen timber adversely affect floodplain ecosystems around the world. Studies of the dynamics of floodplain-dwelling populations will help to understand the effects of altered flood regimes and to manage and restore floodplains. The yellow-footed antechinus (Antechinus flavipes) is the only small, native, carnivorous mammal (Marsupialia) on many degraded floodplains in south-eastern Australia, where its abundance appears to increase with proximity to floods, which is partly due to enhanced survival (as inferred from increased abundance of second-year females). We analysed population genetic patterns and maternity among samples collected following the period of postnatal dispersal, in the years preceding and following planned floods, at different distances from flood locations along the Murray River. Our genic and genotypic analyses of mitochondrial DNA (mtDNA) control region haplotypes and 11 microsatellite loci demonstrated high immigration rates into sites in close proximity to floods. All sampled males emigrated from their natal sites to points of capture, while some females were philopatric. There were high rates of dispersal of males among all sites within a partially flooded forest, while females dispersed more to locations closest to inundations rather than to distant places. These results suggest that environmental flows are beneficial to antechinus both by enhancing adult survival and promoting dispersal of females.     

Assessing Nuclear and Mitochondrial DNA Sequence Variation Within Steinernema (Rhabditida: Steinernematidae)

DNA sequence analysis was used to characterize the nuclear ribosomal DNA ITS1 region and a portion of the COII and 16S rDNA genes of the mitochondrial genome from Steinernema entomopathogenic nematodes. Nuclear ITS1 nucleotide divergence among seven Steinernema spp. ranged from 6 to 22%, and mtDNA divergence among five species ranged from 12 to 20%. No intraspecific variation was observed among three S. feltiae strains. Phylogenetic analysis of both nuclear and mitochondrial DNA sequences confirms the existing morphological relationships of several Steinernema species. Both the rDNA ITS1 and mtDNA sequences were useful for resolving relationships among Steinernema taxa.     

Segregation of Naturally Occurring Mitochondrial DNA Variants in a Mini-Pig Model

The maternally inherited mitochondrial genome (mtDNA) is present in multimeric form within cells and harbors sequence variants (heteroplasmy). While a single mtDNA variant at high load can cause disease, naturally occurring variants likely persist at low levels across generations of healthy populations. To determine how naturally occurring variants are segregated and transmitted, we generated a mini-pig model, which originates from the same maternal ancestor. Following next-generation sequencing, we identified a series of low-level mtDNA variants in blood samples from the female founder and her daughters. Four variants, ranging from 3% to 20%, were selected for validation by high-resolution melting analysis in 12 tissues from 31 animals across three generations. All four variants were maintained in the offspring, but variant load fluctuated significantly across the generations in several tissues, with sex-specific differences in heart and liver. Moreover, variant load was persistently reduced in high-respiratory organs (heart, brain, diaphragm, and muscle), which correlated significantly with higher mtDNA copy number. However, oocytes showed increased heterogeneity in variant load, which correlated with increased mtDNA copy number during in vitro maturation. Altogether, these outcomes show that naturally occurring mtDNA variants segregate and are maintained in a tissue-specific manner across generations. This segregation likely involves the maintenance of selective mtDNA variants during organogenesis, which can be differentially regulated in oocytes and preimplantation embryos during maturation.     

Zoogeographical implications of variation in mitochondrial DNA of Arctic grayling (Thymallus arcticus)

Most of the northern half of North America's freshwater fish survived the last glacial period in unfrozen refugia peripheral to the ice sheets. In our study, the question of which refugia Arctic grayling ( Thymallus arcticus ) inhabited during the Wisconsinan Ice Age, and how they subsequently dispersed to their present geographical range, was examined using mitochondrial DNA (mtDNA) analysis. mtDNA from 12 T. arcticus populations was analysed by direct sequencing and restriction fragment length polymorphism analysis (RFLP). Our data support the hypotheses that T. arcticus had a large refugial population in the Bering Refuge (shown by high mtDNA diversity in extant Alaskan populations) and that British Columbia was colonized from the Bering Refuge (shown by mtDNA haplotype similarities). Our data also show that a disjunct southern set of populations in Montana is significantly different from the northern grayling, in terms of restriction haplotype frequency and distinguishing sequence characteristics. Sequence results yielded an estimated divergence time of 370 000 years between the northern and Montana grayling haplotypes. We conclude that T. arcticus survived the Wisconsinan glaciation in at least two refugia: (i) the Bering Refuge north of the ice sheets; and (ii) either the Upper Missouri or the southwest Alberta Refuge, south of the ice sheet.