Divergent mtDNA Lineages Research Articles

Genealogy of the nuclear β-fibrinogen locus in a highly structured lizard species: comparison with mtDNA and evidence for intragenic recombination in the hybrid zone

The study of nuclear genealogies in natural populations of nonmodel organisms is expected to provide novel insights into the evolutionary history of populations, especially when developed in the framework of well-established mtDNA phylogeographical scenarios. In the Iberian Peninsula, the endemic Schreiber's green lizard Lacerta schreiberi exhibits two highly divergent and allopatric mtDNA lineages that started to split during the late Pliocene. In this work, we performed a fine-scale analysis of the putative mtDNA contact zone together with a global analysis of the patterns of variation observed at the nuclear beta-fibrinogen intron 7 (beta-fibint7). Using a combination of DNA sequencing with single-strand conformational polymorphism (SSCP) analysis, we show that the observed genealogy at the beta-fibint7 locus reveals extensive admixture between two formerly isolated lizard populations while the two mtDNA lineages remain essentially allopatric. In addition, a private beta-fibint7 haplotype detected in the single population where both mtDNA lineages were found in sympatry is probably the result of intragenic recombination between the two more common and divergent beta-fibint7 haplotypes. Our results suggest that the progressive incorporation of nuclear genealogies in investigating the ancient demography and admixture dynamics of divergent genomes will be necessary to obtain a more comprehensive picture of the evolutionary history of organisms.

Biogeographic history of an Australian freshwater shrimp, Paratya australiensis (Atyidae): the role life history transition in phylogeographic diversification

The widespread distribution of the freshwater shrimp Paratya australiensis in eastern Australia suggests that populations of this species have been connected in the past. Amphidromy is ancestral in these shrimps, although many extant populations are known to be restricted to freshwater habitats. In this study, we used a fragment of the cytochrome c oxidase I mitochondrial DNA (mtDNA) gene to examine diversity within P. australiensis and to assess the relative importance of amphidromy in its evolutionary history. We hypothesized that if transitions from an amphidromous to a freshwater life history were important, then we would find a number of divergent lineages restricted to single or groups of nearby drainages. Alternatively, if amphidromy was maintained within the species historically, we expected to find lineages distributed over many drainages. We assumed that the only way for divergence to occur within amphidromous lineages was if dispersal was limited to between nearby estuaries, which, during arid periods in the earth's history, became isolated from one another. We found nine highly divergent mtDNA lineages, estimated to have diverged from one another in the late Miocene/early Pliocene, when the climate was more arid than at present. Despite this, the geographic distribution of lineages and haplotypes within lineages did not support the notion of a stepping-stone model of dispersal between estuaries. We conclude that the extensive divergence has most likely arisen through a number of independent amphidromy-freshwater life history transitions, rather than via historical isolation of amphidromy populations. We also found evidence for extensive movement between coastal and inland drainages, supporting the notion that secondary contact between lineages may have occurred as a result of drainage rearrangements. Finally, our data indicate that P. australiensis is likely a complex of cryptic species, some of which are widely distributed, and others geographically restricted.

Population Genetics and Identity of an Introduced Terrestrial Slug: Arion subfuscus s.l. in the North-east USA (Gastropoda, Pulmonata, Arionidae)

Several European species of the terrestrial slug genus Arion have been introduced into North America. A case in point is the species complex A. subfuscus s.l. which has become one of the most abundant slug taxa in North America. In Europe this complex consists of at least two cryptic species, viz. A. fuscus and A. subfuscus s.s., the latter of which is further subdivided in five strongly divergent mtDNA lineages (A. subfuscus S1-S5). In order to determine which of these A. subfsucus s.l. taxa are present in the NE USA and in order to assess their population genetic structure, we compared mtDNA, nDNA and allozyme variation between populations from the NE USA and Europe. Our results show that (1) at least A. subfuscus S1 has become successfully established in the NE USA, (2) founder effects are the most likely explanation for the loss of a large amount of molecular genetic variation in populations from the NE USA (i.e. a loss of 96% of the 16S rDNA haplotypes, 67% of the ITS1 alleles and 46% of the alleles at polymorphic allozyme loci), and (3) part of the remaining genetic variation in NE USA populations was probably due to multiple introductions from the British Isles and the European mainland, and the hybrid structure of most of these source populations. Apparently, the extreme loss of molecular genetic variation in this introduced species has not prevented it from successfully establishing and spreading in novel environments.

Molecular phylogeny of fire ants of the Solenopsis saevissima species-group based on mtDNA sequences

The systematics of South American fire ants ( Solenopsis saevissima species-group) has been plagued by difficulties in recognizing species and their relationships on the basis of morphological characters. We surveyed mtDNA sequences from 623 individuals representing 13 described and undescribed species within the species-group and 18 individuals representing other major Solenopsis lineages to generate a phylogeny of the mitochondrial genome. Our analyses support the monophyly of the S. saevissima species-group, consistent with a single Neotropical origin and radiation of this important group of ants, as well as the monophyly of the socially polymorphic species within the group, consistent with a single origin of polygyny (multiple queens per colony) as a derived form of social organization. The mtDNA sequences of the inquiline social parasite S. daguerrei form a clade that appears to be distantly related to sequences from the several host species, consistent with the view that advanced social parasitism did not evolve via sympatric speciation of intraspecific parasites. An important general finding is that species-level polyphyly of the mtDNA appears to be the rule in this group of ants. The existence of multiple divergent mtDNA lineages within several nominal species (including the pest S. invicta) suggests that the pattern of widespread polyphyly often stems from morphological delimitation that overcircumscribes species. However, in two cases the mtDNA polyphyly likely results from recent interspecific hybridization. While resolving species boundaries and relationships is important for understanding general patterns of diversification of South American fire ants, these issues are of added importance because invasive fire ants are emerging as global pests and becoming important model organisms for evolutionary research.

Molecular phylogenetics of Gymnocypris (Teleostei: Cy-prinidae) in Lake Qinghai and adjacent drainages

149 complete mitochondrial DNA (mtDNA) cytochrome b (Cyt b) genes (1140 bp) of Gymnocypris przewalskii, Gymnocypris eckloni and Gymnocyptis scolistomus from the Lake Qinghai, Yellow River and Qaidam Basin were sequenced and analyzed. Consistent dendrogram indicated that the samples collected from the same species do not constitute a separate monophyletic group and all the samples were grouped into three highly divergent lineages (A, B and C). Among them, Lineage A contained all samples of G. przewalskii from the Lake Qinghai and partial samples of the G. eckloni from the Yellow River. Lineage B contained the remaining samples of G. eckloni from the Yellow River. Lineage C was composed of a monophyletic group by G. eckloni from the Qaidam Basin. Analysis of molecular variance (AMOVA) indicated that most of genetic variations were detected within these three mtDNA lineages (93.12%), suggesting that there are three different lineages of Gymnocypris in this region. Our Cyt b sequence data showed that G. przewalskii was not a polytypic species, and G. scolistomus was neither an independent species nor a subspecies of G. eckloni. The divergent mtDNA lineages of G. eckloni from the Yellow River suggested that gene flow between the different populations was restricted to a certain extent by several gorges on the upper reach of the Yellow River. Lineage B of G. eckloni might be the genetic effect from the ancestor which was incorporated with the endemic schizothoracine fishes when the headward erosion of the Yellow River reached to its current headwaters of late. The G. eckloni from Basin Qaidam was a monophyletic group (lineage C) and F-st values within G. eckloni from the Yellow River were higher than 0.98, suggesting that the gene flow has been interrupted for a long time and the G. eckloni from Basin Qaidam might have been evolved into different species by ecology segregation. The correlation between the rakers number of Gymnocypris and population genetic variation was not significant. All Gymnocypris populations exhibited a low nucleotide diversity (pi = 0.00096-0.00485). Therefore the Gymnocyptis populations from Basin Qaidam could have experienced severe bottleneck effect in history. Our result suggested Gym-nocypris populations of Basin Qaidam should give a high priority in conservation programs.

Association of genetic lineages with ecological features in a polyphagous montane grasshopper species

Abstract Understanding the relationships between intraspecific diversity and habitat has been greatly enhanced with the advent of molecular markers. Such understanding may help to elucidate complex microevolutionary processes. Melanoplus alpinus, a montane/alpine grasshopper species found in the central and northern Rocky Mountains, has a disjunct distribution with highly divergent mtDNA lineages, structured among meadows and drainages within mountain ranges. Previous analyses showed that genetic differentiation is not distance driven, so habitat factors may account for genetic structuring and diversity within the species. In this study, 3 mtDNA lineages were analyzed for their association with ecological variables, and PCR-RFLP haplotype genetic diversities were analyzed for relationships with elevation, elevation-latitude index, and meadow size. Chi-square analysis revealed mtDNA lineage predominance in particular soil textures, indicating the potential of soil to function as a limiting environmental fa...

Phylogeography ofBufo fowleriat its northern range limit

Many of the species that recolonized previously glaciated areas in the Great Lakes basin of North America over the past 10-12,000 years exhibit genetic evidence of multiple invasion routes and present-day secondary contact between deeply divergent lineages. With this in mind, we investigated the phylogeographical structure of genetic variability in Fowler's toads (Bufo fowleri) at the northern edge of its distribution where its range encircles the Lake Erie basin. Because B. fowleri is so closely tied to habitats along the Lake Erie shoreline, we would expect to find clear evidence of the number of invasions leading to the species' colonization of the northern shore. A 540 bp sequence from the mitochondrial control region was amplified and analysed for 158 individuals from 21 populations. Interpopulation sequence variation ranged from 0% to 6%. Phylogenetic analysis of p-distance using the neighbor-joining method revealed two deeply divergent (6% sequence divergence) mtDNA lineages (Phylogroup 1 and 2), possibly arising as a result of secondary contact of populations that entered the region from two separate glacial refugia. However, the phylogeographical pattern was not simple. The populations at Long Point, on the north shore of Lake Erie, clustered with the population from Indiana Dunes on Lake Michigan to form Phylogroup 2 whereas all other B. fowleri populations examined from both sides of Lake Erie constituted Phylogroup 1. Furthermore, mtDNA sequences from the related species Bufo americanus, obtained from populations outside the range of B. fowleri, clustered with mtDNA haplotypes of B. fowleri Phylogroup 1, indicating the possibility of partial introgression of mitochondria from one species to the other.

Biogeographic patterns and current distribution of molecular-genetic variation among populations of speckled dace, Rhinichthys osculus (Girard)

We examined genetic diversity within- and among-populations of speckled dace ( Rhinichthys osculus) in five major drainage systems in the state of Oregon in western North America. Analysis of sequence variation in a 670-bp segment of the mitochondrial cytochrome b gene revealed deep divergence among basins and high genetic diversity within basins. Application of a molecular clock indicated that the divergence time among basins reflects vicariant events during the late Miocene to early Pliocene. The high levels of genetic diversity observed within basins is likely due to large historic population sizes, in particular, within the Klamath Basin. Two highly divergent mtDNA lineages were found to co-occur in populations in the Klamath Basin. This result may be indicative of a complex history of isolation and reconnection in this basin and/or multiple colonization events. Based on the observed level of mtDNA divergence these lineages may represent two reproductively isolated sympatric taxa. We recommend that major basins be regarded as distinct ESUs based on high levels of subdivision, deep divergences, and reciprocal monophyly among basins.

Population structure of two ecologically distinct forms of ninespine stickleback,Pungitius pungitius: gene flow regimes and genetic diversity based on mtDNA sequence variations

The population structure and its effect on genetic diversity were investigated in two ecologically distinct forms (fresh- and brackish-water types) of ninespine stickleback (Pungitius pungitius L.), which coexist on the coast of eastern Hokkaido, Japan. Obvious population subdivision (φST= 0.102 to 0.668) between freshwater systems in the freshwater type compared with that in the brackish-water type (φST= <0 to 0.078) was revealed on the basis of mitochondrial DNA (mtDNA) control region sequence variations. Results of the nested clade analysis suggested that the geographic distribution patterns of mtDNA lineages were mainly due to the contemporary population structure, rather than population histories. Although local populations were sampled from a similar geographic range for the two types, gene and nucleotide diversities of the freshwater type were significantly greater (0.94 and 0.016) than those of the brackish-water type (0.55 and 0.003). The increment of genetic diversity should be attributable to the obvious population structure and existence of divergent mtDNA lineages in the former, which clearly increased the effective population size of a subdivided population. Although these two forms maintain distinct gene pools, small sequence differences among mtDNA haplotypes obtained from each type suggested that mtDNA introgression has occurred between them.

Speciation and phylogeography in Caridina indistincta, a complex of freshwater shrimps from Australian heathland streams

The Caridina indistincta complex is a group of closely related atyid shrimps that inhabit coastal freshwater streams throughout north-eastern Australia. Using mitochondrial DNA sequence data (cytochrome oxidase 1, CO1), we (1) inferred the timing of speciation in the C. indistincta group and (2) examined the intraspecific phylogeographic patterns within the group. Assuming a shrimp-specific rate of CO1 evolution, the level of sequence divergence among species suggests that speciation took place during the Miocene epoch. Within one widespread mainland species, phylogeographic patterns suggest strong geographic 'regionalisation' of mtDNA lineages that are most likely of Pleistocene origin. By contrast, another species comprises two highly divergent mtDNA lineages that occur in sympatry. We suggest that although Pleistocene sea-level regressions appear important in generating population-level phylogeographic patterns, these events were largely unimportant in the formation of species in this group.

Cryptic speciation in the Anadenobolus excisus millipede species complex on the Island of Jamaica.

Anadenobolus excisus is a large species of millipede endemic to the Caribbean Island of Jamaica. Initial detailed morphological studies showed little or no discrete variation across this species' distribution in somatic or, in particular. genitalic morphology. However, a molecular survey based on approximately 1000 base pairs of the mitochondrial (mtDNA) 16S rRNA gene that examines 242 individuals sampled from 54 localities reveals three highly divergent mtDNA lineages. A lack of discrete morphological differentiation suggests that genetic and morphological divergence may be decoupled, a pattern inconsistent with a number of evolutionary models. In contrast to minimal morphological divergence, size variation among mtDNA lineages suggests that character displacement has occurred and that these lineages are cohesive in sympatry. We conclude that A. excisus is actually a complex of three cryptic species and that morphological approaches to delineating millipede species may sometimes underestimate evolutionary diversity.

CRYPTIC SPECIATION IN THE ANADENOBOLUS EXCISUS MILLIPEDE SPECIES COMPLEX ON THE ISLAND OF JAMAICA

Anadenobolus excisus is a large species of millipede endemic to the Caribbean Island of Jamaica. Initial detailed morphological studies showed little or no discrete variation across this species' distribution in somatic or, in particular, genitalic morphology. However, a molecular survey based on ∼1000 base pairs of the mitochondrial (mtDNA) 16S rRNA gene that examines 242 individuals sampled from 54 localities reveals three highly divergent mtDNA lineages. A lack of discrete morphological differentiation suggests that genetic and morphological divergence may be decoupled, a pattern inconsistent with a number of evolutionary models. In contrast to minimal morphological divergence, size variation among mtDNA lineages suggests that character displacement has occurred and that these lineages are cohesive in sympatry. We conclude that A. excisus is actually a complex of three cryptic species and that morphological approaches to delineating millipede species may sometimes underestimate evolutionary diversity.

Genetic diversity of North American populations of Cristatella mucedo, inferred from microsatellite and mitochondrial DNA.

Research over the past 20 years has shown, with the help of molecular markers, that the population genetics and distribution patterns of freshwater invertebrates in North America are often more complex than was previously believed. Here we extend this research to an, as yet, unstudied but widespread and common group, the freshwater bryozoans. Colonies of the bryozoan Cristatella mucedo were collected from a number of lakes across central North America, and were characterized genetically by analysis of microsatellite loci and mitochondrial DNA (mtDNA) cytochrome b sequences. The microsatellites illustrate a pattern of generally diverse and highly differentiated populations that contain little evidence of recent gene flow. The mtDNA sequences yielded highly variable levels of divergence, ranging from 0.0 to 8.8% within populations, and 0.0 to 9.8% among populations. The multiple divergent mtDNA lineages within populations provide evidence for repeated colonization events. The lack of clustering of haplotypes by site suggests that there has been widespread dispersal of multiple genetic lineages since the last ice age. While some of the haplotype lineages may have evolved in disjunct glacial refugia, the maximum levels of divergence predate the time since the last glacial-interglacial cycles. It is likely that multiple factors including vicariance events, patterns of dispersal, localized extinction, and an unusual life history, explain the unique phylogeographic patterns evident today in populations of C. mucedo.

Mitochondrial DNA and chromosomal studies of wild mice (Mus) from Turkey and Iran.

Complete D-loop sequences of 20 Mus from three localities in Turkey and seven in Iran were characterized. These countries are thought to be close to the place of origin of the subspecies Mus musculus domesticus. Five new M. m. domesticus haplotypes were added to the nine already known for the region. Four of these 14 haplotypes were very similar to the consensus D-loop sequence for western Europe defined by Nachman et al. (1994), which may represent the ancestral condition for M. m. domesticus. A divergent mtDNA lineage is found in various parts of Turkey and northern Iran; it has spread into western Europe, but other European lineages were not found in either Turkey or Iran. The other Mus D-loop sequences were of M. m. castaneus and Mus macedonicus and confirmed M. macedonicus as a monotypic species with low nucleotide diversity. The prevalence of the standard 40-chromosome complement in this region is particularly interesting with regards M. m. domesticus, as it is consistent with the in situ origin of Robertsonian karyotypic races (2n < 40) in western Europe.

Phylogeography of the canyon treefrog, Hyla arenicolor (Cope) based on mitochondrial DNA sequence data.

Patterns of phylogeography and gene flow were examined in the canyon treefrog, Hyla arenicolor. A total of 973 bp of mitochondrial cytochrome b sequence data were obtained for 65 individuals from 53 populations, yielding 50 unique haplotypes. Interpopulation sequence variation ranged from 0 to 13.7%. Phylogenetic analysis revealed three deeply divergent mtDNA lineages. These three Clades were mapped onto geography and found to represent completely concordant, nonoverlapping, geographical regions. Levels of sequence divergence between the three Clades were equal to or greater than published levels of divergence found in other vertebrate species and genera. Furthermore, one Clade of H. arenicolor was found to be more closely related to the outgroup H. eximia than to other H. arenicolor, suggesting that the taxonomy of this species may require revision.

PARALLEL EVOLUTION OF LAKE-STREAM PAIRS OF THREESPINE STICKLEBACKS (GASTEROSTEUS) INFERRED FROM MITOCHONDRIAL DNA VARIATION.

Three drainage systems in British Columbia, Canada, contain divergent parapatric lake-stream pairs of threespine sticklebacks (Gasterosteus aculeatus): Drizzle and Mayer Lakes on Graham Island, Queen Charlotte Islands, and Misty Lake on northeastern Vancouver Island. Ecological and morphological differences between members of all three lake-stream pairs are strikingly similar; lake fish are melanistic and slim bodied with smaller mouths and more gill rakers than the mottled-brown and robust-bodied stream sticklebacks. We estimated the level of genetic divergence between lake and stream fish in Misty Lake and tested hypotheses of single versus multiple origins of the pairs by assaying mitochondrial DNA (mtDNA) restriction site variation in samples from the three lake systems. MtDNA analysis revealed the existence of two highly divergent lineages differing by 2.7% in sequence. One lineage predominated in Misty stream fish (73%), whereas the other lineage predominated in Misty Lake samples (96%). Comparable forms (lake or stream) in the different lakes did not cluster together in terms of mtDNA nucleotide divergence, suggesting that the pairs have had independent origins. We concluded that: (1) divergent mtDNA lineages in North Pacific sticklebacks stem from historical isolation in the two major glacial refugia proposed for the North Pacific (Beringia and Cascadia); (2) the stream and lake pair in Misty Lake are distinct gene pools; (3) the divergence between parapatric lake and stream Gasterosteus represents parallel evolution having occurred at least twice in the North Pacific; and (4) different scales of evolutionary divergence exist in North Pacific Gasterosteus, that is, a relatively ancient divergence of mtDNA clades as well as recent (i.e., postglacial) divergence of ecotypes within major clades.

Genetic population structure of the Greater Bilby Macrotis lagotis, a marsupial in decline.

The Greater Bilby has shown a rapid decline in range during this century and now occupies only a small isolated area in south-western Queensland (QLD) and a larger, but mostly low-density area in the north-western deserts of the Northern Territory (NT) and Western Australia (WA). We have examined variation in the control region of mitochondrial DNA (mtDNA) and at nine microsatellite loci in order to investigate the extent of current and historical subdivision across the species range, and to provide a preliminary assessment of genetic structuring and mating system on a finer scale within the QLD population. Both mtDNA and microsatellite loci had substantial variation within and among populations, with mtDNA divergence being greater between QLD and NT than between NT and WA. The QLD population had two unique and divergent mtDNA lineages, but there was no evidence for strong phylogeographical structure across the range. The available evidence suggests that the bilby should be considered as a single Evolutionarily Significant Unit consisting of multiple Management Units. Augmentation of the remnant QLD population from the NT does not appear necessary at this stage, at least not on genetic grounds. Finer-scale analysis of microsatellite variation for two QLD colonies revealed a deficiency of heterozygotes and significantly greater relatedness within than between colonies. However, structuring was observed only for males; relatedness values for females did not depart from those expected under panmixia. Parentage exclusion analysis for one colony allowed the construction of a partial pedigree which indicated strong polygyny, with one male fathering all but one of the eight offspring assigned. The extent to which fine-scale genetic structuring and differences between sexes is due to sex-biased dispersal vs. effects of mating system remain to be determined.

Origins of endemic stickleback from the Queen Charlotte Islands: mitochondrial and morphological evidence

Recently, two divergent mitochondrial lineages were described in a survey of 12 scattered populations of the threespine stickleback (Gasterosteus aculeatus) on the Queen Charlotte Islands (QCI), western Canada, one of which, possibly a relict lineage, was subsequently shown to characterize stickleback from the western Pacific near Japan. In the present study, we assayed 985 fish from 85 QCI populations for mitochondrial lineage using a restriction enzyme test. Our data indicate that the relict lineage was largely limited (18 of 20 populations) to adjacent watersheds in the northeast corner of the QCI close to a suspected glacial refugium, but we also found the lineage in two remote lakes on the west coast of the QCI, distant from any known refugia. We obtained a sample of 33 stickleback from the mid-Pacific and found both mitochondrial DNA (mtDNA) lineages, strongly suggesting ongoing dispersal of these fish across the Pacific, and inconsistent with previous suggestions of relict status for one of the lineages. Morphologically derived traits, such as loss of armour and loss of spines, occurred in both lineages, but these were more prevalent in the Japanese lineage. Surprisingly, 19 localities had both lineages, and within each of these there were no significant univariate or multivariate associations between lineages and morphology, suggesting few if any reproductive barriers between the divergent mtDNA lineages.