PERCHED AT THE MITO‐NUCLEAR CROSSROADS: DIVERGENT MITOCHONDRIAL LINEAGES CORRELATE WITH ENVIRONMENT IN THE FACE OF ONGOING NUCLEAR GENE FLOW IN AN AUSTRALIAN BIRD

Relationships among multilocus genetic variation, geography, and environment can reveal how evolutionary processes affect genomes. We examined the evolution of an Australian bird, the eastern yellow robin Eopsaltria australis, using mitochondrial (mtDNA) and nuclear (nDNA) genetic markers, and bioclimatic variables. In southeastern Australia, two divergent mtDNA lineages occur east and west of the Great Dividing Range, perpendicular to latitudinal nDNA structure. We evaluated alternative scenarios to explain this striking discordance in landscape genetic patterning. Stochastic mtDNA lineage sorting can be rejected because the mtDNA lineages are essentially distinct geographically for > 1500 km. Vicariance is unlikely: the Great Dividing Range is neither a current barrier nor was it at the Last Glacial Maximum according to species distribution modeling; nuclear gene flow inferred from coalescent analysis affirms this. Female philopatry contradicts known female‐biased dispersal. Contrasting mtDNA and nDNA demographies indicate their evolutionary histories are decoupled. Distance‐based redundancy analysis, in which environmental temperatures explain mtDNA variance above that explained by geographic position and isolation‐by‐distance, favors a nonneutral explanation for mitochondrial phylogeographic patterning. Thus, observed mito‐nuclear discordance accords with environmental selection on a female‐linked trait, such as mtDNA, mtDNA–nDNA interactions or genes on W‐chromosome, driving mitochondrial divergence in the presence of nuclear gene flow.     

A mitogenomic study on the phylogenetic position of snakes

Phylogenetic relationships of squamates (lizards, amphisbaenians and snakes) have received considerable attention, although no consensus has been reached concerning some basal divergences. This paper focuses on the Serpentes (snakes), whose phylogenetic position within the Squamata remains uncertain despite a number of morphological and molecular studies. Some mitogenomic studies have suggested a sister-group relationship between snakes and varanid lizards, while other studies have identified snakes and lizards as sister groups. However, recent studies using nuclear data have presented a different scenario, with snakes being more closely related to anguimorph and iguanian lizards. In this mitogenomic study we have examined the above hypotheses with the inclusion of amphisbaenians, one gekkotan and one acrodont lizard, taxa not represented in previous mitogenomic studies. To this end we have also extended the representation of snakes by sequencing five additional snake genomes: two scolecophidians ( Ramphotyphlops australis and Typhlops mirus ) two henophidians ( Eunectes notaeus and Boa constrictor ) and one caenophidian ( Elaphe guttata ). The phylogenetic analysis recovered snakes and amphisbaenians as sister groups, thereby differing from previous hypotheses. In addition to a discussion on previous morphological and molecular studies in light of the results presented here, the current study also provides some details regarding features of the new snake mitochondrial genomes described.     

Simultaneous extraction of nuclear and mitochondrial DNA from human blood

A method of simultaneous isolation of nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) from human blood has been proposed by improvising Lahiri's method of isolation of nuclear DNA. The approach presented here provides selectively enriched fractions and eliminates the need for two different methods or separate reagent sets for the extraction of nDNA and mtDNA. It employs an initial nuclear/ cytoplasm partitioning, followed by the similar procedural steps for the two fractions separately. It gives good quality and quantity of the nDNA as well as the mtDNA, suitable for processes like PCR amplification and sequencing and may prove to be useful for people studying population genetics and evolution using molecular markers maximizing the available resources, especially in cases where a large database needs to be generated from limited amount of blood sample. From 3 ml of blood, the yields of mtDNA salvaged from the supernatant were sufficient to set approximately 4x10(5) reactions (starting with 250 fg DNA per reactions) of mtDNA loci which otherwise would have been discarded as per original Lahiri's procedure. The quality of mtDNA from the mitochondrial fraction was suitable for all major downstream processes as confirmed by locus specific PCR amplifications and sequencing. Through this procedure, the wastage of nDNA can be avoided when mtDNA loci is studied.     

Hybridization between mtDNA-defined phylogeographic lineages of black ratsnakes (Pantherophis sp.)

Phylogeographic analyses using mitochondrial DNA (mtDNA) have revealed many examples of apparently deep historical subdivisions ('phylogroups') within many vertebrates. It remains unclear whether these phylogroups represent independently evolving, adaptively differentiated lineages or groups that show little functional differentiation and, hence, will merge on contact. Here, we use mtDNA sequence data to evaluate the phylogeographic relationships between two of the northernmost populations of black ratsnakes (Pantherophis obsoletus complex) in Ontario, Canada and previously analysed populations in the United States. We then use population-level analyses to evaluate the level of adaptive divergence between previously established mtDNA phylogroups. Phylogenetic analyses show that southern Ontario snakes have mtDNA haplotypes that fall within the Central mtDNA phylogroup, as designated by Burbrink et al. (2000). In contrast, snakes in eastern Ontario carry either Central or Eastern-specific haplotypes. Within the hybrid region, we found highly variable frequencies of mtDNA haplotypes among isolated sub-populations, no association between variation in cytonuclear (mtDNA) and nuclear (microsatellite DNA) markers, no difference in survival or reproductive success among snakes with different mtDNA haplotypes, and no effect of mate similarity in mtDNA on female clutch size. These results argue that the Eastern and Central phylogroups have merged in this region, likely due to a lack of adaptive differentiation between individuals in each lineage. Hence, in these snakes, phylogeographic structure in mtDNA is more a reflection of historical isolation rather than adaptive divergence. The observed reticulation between lineages and lack of evidence for hybrid disgenesis also bears on the classification of these lineages as distinct species.     

Genetic characterization of Amur sturgeon <Emphasis Type="Italic">Acipenser schrenckii</Emphasis> and its hybrid caught around Hokkaido

Genetic characterization was performed in five individuals of wild Amur sturgeon Acipenser schrenckii, and/or its presumed hybrid caught around Hokkaido, using a mitochondrial DNA (mtDNA) marker and two markers of nuclear DNA (nDNA). Genetic analyses indicated that two of the five fish had the mtDNA haplotype of Kaluga, Huso dauricus, whereas the nDNA markers indicated signs for both A. schrenckii and H. dauricus genotypes, referring to a hybrid origin. The other three fish were plausibly pure A. schrenckii. The results indicated the importance of combined usage of mtDNA and nDNA markers for correct species identification in sturgeon.     

Diversity and demography in Beringia: multilocus tests of paleodistribution models reveal the complex history of arctic ground squirrels

To assess effects of historical climate change on northern species, we quantified the population history of the arctic ground squirrel (Spermophilus parryii), an arctic-adapted rodent that evolved in Beringia and was strongly influenced by climatic oscillations of the Quaternary. Competing hypotheses for the species' population history were derived from patterns of mitochondrial (mtDNA) structure and a bioclimatic envelope model (BEM). Hypotheses invoked (1) sequential isolation of regional populations beginning with the Arctic, (2) deep isolation only across central Alaska, and (3) widespread panmixia, and were tested using coalescent methods applied to eight nuclear (nDNA) loci. The data rejected strict interpretations of all three hypotheses, but perspectives underlying each encompassed aspects of the species' history. Concordance between mtDNA and nDNA geographic structure revealed three semi-independently evolving phylogroups, whereas signatures of gene flow at nDNA loci were consistent with a historical contact between certain populations as inferred by the BEM. Demographic growth was inferred for all regions despite expectations of postglacial habitat contraction for parts of Beringia. Our results highlight the complementary perspectives on species' histories that multiple lines of evidence provide, and underscore the utility of multilocus data for resolving complex population histories relevant to understanding effects of climate change.     

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

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

The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a medically important snake, Trimeresurus albolabris

There are a huge number of phylogenetic studies based on mitochondrial DNA (mtDNA); however, these may represent gene trees that may not be congruent with the species tree. A solution to this problem is to include additional, independent, loci from the nuclear genome. At fine taxonomic levels, i.e. between populations and closely related species, previously suggested nuclear markers such as intron sequence data may not be appropriate. In this study we investigate the use of amplified fragment length polymorphisms (AFLP) to aid determination of the species tree for 24 specimens of a medically important snake, Trimeresurus albolabris. This is of particular importance for many venomous snakes as venom often varies intraspecifically. Five different primer combinations produced 434 bands and were analysed by constructing a phylogenetic tree using neighbour joining and principal component analysis. Results were similar across all methods and found distinct groupings. The results were compared with mtDNA data and a reconciled tree was constructed in order to determine the species tree for T. albolabris. We found that T. albolabris (sensu lato) is not monophyletic. Specimens from the Indonesian islands (except West Java) form a distinct clade and we propose elevation to species level. A specimen from Nepal is also distinct and suggests that this population also deserves specific status. We suggest that AFLPs may prove a valuable aid in determining species trees as opposed to gene trees at fine taxonomic levels and this should facilitate the incorporation of molecular data into such activities as antivenom production and conservation management.     

Multi-locus DNA sequence data reveal a history of deep cryptic vicariance and habitat-driven convergence in the desert night lizard Xantusia vigilis species complex (Squamata: Xantusiidae)

The lizard genus Xantusia of southwestern North America has received recent attention in relation to delimiting species. Using more than 500 lizards from 156 localities, we further test hypothesized species boundaries and clarify phylogeographical patterns, particularly in regions of potential secondary contact. We sequenced the entire mitochondrial cytochrome b gene for every lizard in the study, plus a second mitochondrial DNA (mtDNA) region and two nuclear introns for subsets of the total sample. Phylogenetic analyses of the mtDNA recover a well-resolved, novel hypothesis for species in the Xantusia vigilis complex. The nuclear DNA (nDNA) data provide independent support for the recognition of X. arizonae, X. bezyi and X. wigginsi. Differences between the respective mtDNA and nDNA topologies result from either the effects of lineage sorting or ancient introgression. Nuclear data confirm the inference that some populations of X. vigilis in northwestern Arizona converged on rock-crevice-dwelling morphology and are not X. arizonae with an introgressed X. vigilis mtDNA genome. The historical independence of ancient cryptic lineages of Xantusia in southern California is also corroborated, though limited introgression is detected. Our proposed biogeographical scenario indicates that diversification of this group was driven by vicariance beginning in the late Miocene. Additionally, Pleistocene climatical changes influenced Xantusia distribution, and the now inhospitable Colorado Desert previously supported night lizard presence. The current taxonomy of the group likely underestimates species diversity within the group, and our results collectively show that while convergence on the rock-crevice-dwelling morphology is one hallmark of Xantusia evolution, morphological stasis is paradoxically another.     

Origin and phylogeography of African savannah elephants (<Emphasis Type="Italic">Loxodonta africana</Emphasis>) in Kruger and nearby parks in southern Africa

African savannah elephants (Loxodonta africana) occur in fragmented and isolated populations across southern Africa. Transfrontier conservation efforts aim at preventing the negative effects of population fragmentation by maintaining and restoring linkages between protected areas. We sought to identify genetic linkages by comparing the elephants in Kruger National Park (South Africa) to populations in nearby countries (Botswana, Mozambique, Zambia and Zimbabwe). We used a 446 base pair mitochondrial DNA (mtDNA) control region fragment (141 individuals) and 9 nuclear DNA (nDNA) microsatellite markers (69 individuals) to investigate phylogenetic relationships and gene flow among elephant populations. The mtDNA and nDNA phylogeographic patterns were incongruent, with mtDNA patterns likely reflecting the effects of ancient female migrations, with patterns persisting due to female philopatry, and nDNA patterns likely reflecting male-mediated dispersal. Kruger elephant heterozygosity and differentiation were examined, and were not consistent with genetic isolation, a depleted gene pool or a strong founder effect. Mitochondrial DNA geographic patterns suggested that the Kruger population was founded by elephants from areas both north and south of Kruger, or has been augmented through migration from more than one geographic source. We discuss our findings in light of the need for conservation initiatives that aim at maintaining or restoring connectivity among populations. Such initiatives may provide a sustainable, self-regulating management approach for elephants in southern Africa while maintaining genetic diversity within and gene flow between Kruger and nearby regions.     

Mitochondrial DNA under siege in avian phylogeography

Mitochondrial DNA (mtDNA) has been the workhorse of research in phylogeography for almost two decades. However, concerns with basing evolutionary interpretations on mtDNA results alone have been voiced since the inception of such studies. Recently, some authors have suggested that the potential problems with mtDNA are so great that inferences about population structure and species limits are unwarranted unless corroborated by other evidence, usually in the form of nuclear gene data. Here we review the relative merits of mitochondrial and nuclear phylogeographical studies, using birds as an exemplar class of organisms. A review of population demographic and genetic theory indicates that mitochondrial and nuclear phylogeographical results ought to concur for both geographically unstructured populations and for populations that have long histories of isolation. However, a relatively common occurrence will be shallow, but geographically structured mtDNA trees--without nuclear gene corroboration--for populations with relatively shorter periods of isolation. This is expected because of the longer coalescence times of nuclear genes (approximately four times that of mtDNA); such cases do not contradict the mtDNA inference of recent isolation and evolutionary divergence. Rather, the nuclear markers are more lagging indicators of changes in population structure. A review of the recent literature on birds reveals the existence of relatively few cases in which nuclear markers contradict mitochondrial markers in a fashion not consistent with coalescent theory. Preliminary information from nuclear genes suggests that mtDNA patterns will prove to be robust indicators of patterns of population history and species limits. At equilibrium, mitochondrial loci are generally a more sensitive indicator of population structure than are nuclear loci, and mitochondrial estimates of F(ST)-like statistics are generally expected to exceed nuclear ones. Hence, invoking behavioural or ecological explanations of such differences is not parsimonious. Nuclear genes will prove important for quantitative estimates of the depths of haplotype trees, rates of population growth and values of gene flow.     

Is homoplasy or lineage sorting the source of incongruent mtdna and nuclear gene trees in the stiff-tailed ducks (Nomonyx-Oxyura)?

We evaluated the potential effects of homoplasy, ancestral polymorphism, and hybridization as obstacles to resolving phylogenetic relationships within Nomonyx-Oxyura stiff-tailed ducks (Oxyurinae; subtribe Oxyurina). Mitochondrial DNA (mtDNA) control region sequences from 94 individuals supported monophyly of mtDNA haplotypes for each of the six species and provided no evidence of extant incomplete lineage sorting or inter-specific hybridization. The ruddy ducks (O. j. jamaicensis,O. j. andina, O. j. ferruginea) are each others' closest relatives, but the lack of shared haplotypes between O. j. jamaicensis and O. j. ferruginea suggests long-standing historical isolation. In contrast, O. j. andina shares haplotypes with O. j. jamaicensis and O. j. ferruginea, which supports Todd's (1979) and Fjelds?'s (1986) hypothesis that O. j. andina is an intergrade or hybrid subspecies of O. j. jamaicensis and O. j. ferruginea. Control region data and a much larger data set composed of approximately 8800 base pairs of mitochondrial and nuclear sequence for each species indicate that the two New World species, O. vittata and O. jamaicensis, branch basally within Oxyura. A clade of three Old World species (O. australis, O. maccoa, O. leucocephala) is well supported, but different loci and also different characters within the mtDNA data support three different resolutions of the Old World clade, yielding an essentially unresolved trichotomy. Fundamentally different factors limited the resolution of the mtDNA and nuclear gene trees. Gene trees for most nuclear loci were unresolved due to slow rates of mutation and a lack of informative variation, whereas uncertain resolution of the mtDNA gene tree was due to homoplasy. Within the mtDNA, approximately equal numbers of characters supported each of three possible resolutions. Parametric and nonparametric bootstrap analyses suggest that resolution of the mtDNA tree based on ~4300 bp per taxon is uncertain but that complete mtDNA sequences would yield a fully resolved gene tree. A short internode separating O. leucocephala from (O. australis, O. maccoa) in the best mtDNA tree combined with long terminal branches and substantial rate variation among nucleotide sites allowed the small number of changes occurring on the internode to be obscured by homoplasy in a significant portion of simulated data sets. Although most nuclear loci were uninformative, two loci supported a resolution of the Old World clade (O. maccoa, O. leucocephala) that is incongruent with the best mtDNA tree. Thus, incongruence between nuclear and mtDNA trees may be due to random sorting of ancestral lineages during the short internode, homoplasy in the mtDNA data, or both. The Oxyura trichotomy represents a difficult though likely common problem in molecular systematics. Given a short internode, the mtDNA tree has a greater chance of being congruent with the history of speciation because its effective population size (N(e)) is one-quarter that of any nuclear locus, but its resolution is more likely to be obscured by homoplasy. In contrast, gene trees for more slowly evolving nuclear loci will be difficult to resolve due to a lack of substitutions during the internode, and when resolved are more likely to be incongruent with the species history due to the stochastic effects of lineage sorting. We suggest that researchers consider first whether independent gene trees are adequately resolved and then whether those trees are congruent with the species history. In the case of Oxyura, the answer to both questions may be no. Complete mtDNA sequences combined with data from a very large number of nuclear loci may be the only way to resolve such trichotomies.     

Examining the utility of categorical models and alleviating artifacts in phylogenetic reconstruction of the Squamata (Reptilia)

Reconstruction artifacts are a serious hindrance to the elucidation of phylogenetic relationships and a number of methods have been devised to alleviate them. Previous studies have demonstrated a striking disparity in the evolutionary rates of the mitochondrial (mt) genomes of squamate reptiles (lizards, worm lizards and snakes) and the reconstruction artifacts that may arise from this. Here, to examine basal squamate relationships, we have added the mt genome of the blind skink Dibamus novaeguineae to the mitogenomic dataset and applied different models for resolving the squamate tree. Categorical models were found to be less susceptible to artifacts than were the commonly used noncategorical phylogenetic models GTR and mtREV. The application of different treatments to the data showed that the removal of the fastest evolving sites in snakes improved phylogenetic signal in the dataset. Basal divergences remained, nevertheless, poorly resolved. The proportion of both fast-evolving and conserved sites in the squamate mt genomes relative to sites with intermediate rates of evolution suggests rapid early divergences among squamate taxa and at least partly explains the short internal relative to external branches in the squamate tree. Thus, mt and nuclear trees may never reach full agreement because of the short branches characterizing these divergences.     

Molecular phylogeny and divergence dates for Australasian elapids and sea snakes (hydrophiinae): evidence from seven genes for rapid evolutionary radiations

One of the most prolific radiations of venomous snakes, the Australo-Melanesian Hydrophiinae includes approximately 100 species of Australasian terrestrial elapids plus all approximately 60 species of viviparous sea snakes. Here, we estimate hydrophiine relationships based on a large data set comprising 5800 bp drawn from seven genes (mitochondrial: ND4, cytb, 12S, 16S; nuclear: rag1, cmos, myh). These data were analysed using parsimony, likelihood and Bayesian methods to better resolve hydrophiine phylogeny and provide a timescale for the terrestrial and marine radiations. Among oviparous forms, Cacophis, Furina and Demansia are basal to other Australian elapids (core oxyuranines). The Melanesian Toxicocalamus and Aspidomorphus group with Demansia, indicating multiple dispersal events between New Guinea and Australia. Oxyuranus and Pseudonaja form a robust clade. The small burrowing taxa form two separate clades, one consisting of Vermicella and Neelaps calanotus, and the other including Simoselaps, Brachyurophis and Neelaps bimaculatus. The viviparous terrestrial elapids form three separate groups: Acanthophis, the Rhinoplocephalus group and the Notechis-Hemiaspis group. True sea snakes (Hydrophiini) are robustly united with the Notechis-Hemiaspis group. Many of the retrieved groupings are consistent with previous molecular and morphological analyses, but the polyphyly of the viviparous and burrowing groups, and of Neelaps, are novel results. Bayesian relaxed clock analyses indicate very recent divergences: the approximately 160 species of the core Australian radiation (including sea snakes) arose within the last 10 Myr, with most inter-generic splits dating to between 10 and 6 Ma. The Hydrophis sea snake lineage is an exceptionally rapid radiation, with > 40 species evolving within the last 5 Myr.     

Polymorphic population genetic markers for the Australian wood cockroach Panesthia australis

Primers for five polymorphic nuclear DNA (nDNA) markers and one mitochondrial DNA (mtDNA) gene (COI) were developed for the Australian wood cockroach Panesthia australis using a range of techniques. Eight mitochondrial haplotypes and four to 36 alleles per nuclear locus were detected in 744 cockroaches. Observed heterozygosity ranged from 0.117 to 0.816 in a sample of 30 animals from one population. The markers will be useful for population biology and for the measurement of the effects of habitat fragmentation on this ecologically important forest‐dependent species.     

Hidden species diversity of Australian burrowing snakes (Ramphotyphlops)

The worm‐like snakes (Scolecophidia; approximately 400 nominal extant species) have a conservative morphology and are among the most poorly‐known terrestrial vertebrates. Although molecular evidence has helped determine their higher‐level relationships, such data have rarely been used to discriminate among species. We generated a molecular data set for the continental Australian blindsnakes (genus Ramphotyphlops) to determine the concordance of molecular and morphological information in the taxonomic recognition of species. Our dataset included 741 specimens morphologically attributed to 27 nominal Ramphotyphlops species. We proposed species hypotheses (SHs) after analysis of sequences from a variable mitochondrial gene (cytochrome b) and examined these SHs with additional evidence from a nuclear gene (prolactin receptor) and geographical data. Although the nuclear marker was not as fast‐evolving and discriminating as the mitochondrial marker, there was congruence among the mitochondrial, nuclear, and geographical data, suggesting that the actual number of species is at least two times the current number of recognized, nominal species. Several biogeographical barriers and complex phytogeographical and geological patterns appeared to be involved in the division of some burrowing snake populations and, by consequence, in their diversification and speciation through isolation. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 427–441.     

Mitochondrial diseases

By convention, the term "mitochondrial diseases" refers to disorders of the mitochondrial respiratory chain, which is the only metabolic pathway in the cell that is under the dual control of the mitochondrial genome (mtDNA) and the nuclear genome (nDNA). Therefore, a genetic classification of the mitochondrial diseases distinguishes disorders due to mutations in mtDNA, which are governed by the relatively lax rules of mitochondrial genetics, and disorders due to mutations in nDNA, which are governed by the stricter rules of mendelian genetics. Mutations in mtDNA can be divided into those that impair mitochondrial protein synthesis in toto and those that affect any one of the 13 respiratory chain subunits encoded by mtDNA. Essential clinical features for each group of diseases are reviewed. Disorders due to mutations in nDNA are more abundant not only because most respiratory chain subunits are nucleus-encoded but also because correct assembly and functioning of the respiratory chain require numerous steps, all of which are under the control of nDNA. These steps (and related diseases) include: (i) synthesis of assembly proteins; (ii) intergenomic signaling; (iii) mitochondrial importation of nDNA-encoded proteins; (iv) synthesis of inner mitochondrial membrane phospholipids; (v) mitochondrial motility and fission.     

Disturbed population genetics: suspected introgressive hybridization between two Mnais damselfly species (Odonata)

Mnais costalis and M. pruinosa are damselflies (Odonata: Calopterygidae) with low dispersal abilities, both during their aquatic stream-living immature stage and their flying adult stage. A previous nuclear DNA (nDNA) sequencing and morphology study showed that these two species are very closely related, and cohabit widely in western Japan. The two species, however, segregate microhabitats along a stream: M. costalis lives in the lower reaches, and M. pruinosa in the upper reaches. In this study, our analyses were based on mitochondrial DNA (mtDNA), which usually mutates faster and is more variable among individuals than nDNA, and which is inherited maternally. We found that most COI haplotypes were shared between the two species, and that for most study sites interspecific riverine genetic structures were not clarified by mtDNA analysis. Incongruent population genetic structures based on nDNA and mtDNA suggested hybridization and introgression of mtDNA between the two species.     

Multiple nuclear gene sequences identify phylogenetic species boundaries in the rapidly radiating clade of Mexican ambystomatid salamanders

Delimiting the boundaries of species involved in radiations is critical to understanding the tempo and mode of lineage formation. Single locus gene trees may or may not reflect the underlying pattern of population divergence and lineage formation, yet they constitute the vast majority of the empirical data in species radiations. In this study we make use of an expressed sequence tag (EST) database to perform nuclear (nDNA) and mitochondrial (mtDNA) genealogical tests of species boundaries in Ambystoma ordinarium, a member of an adaptive radiation of metamorphic and paedomorphic salamanders (the Ambystoma tigrinum complex) that have diversified across terrestrial and aquatic environments. Gene tree comparisons demonstrate extensive nonmonophyly in the mtDNA genealogy of A. ordinarium, while seven of eight independent nuclear loci resolve the species as monophyletic or nearly so, and diagnose it as a well-resolved genealogical species. A differential introgression hypothesis is supported by the observation that western A. ordinarium localities contain mtDNA haplotypes that are identical or minimally diverged from haplotypes sampled from a nearby paedomorphic species, Ambystoma dumerilii, while most nDNA trees place these species in distant phylogenetic positions. These results provide a strong example of how historical introgression can lead to radical differences between gene trees and species histories, even among currently allopatric species with divergent life history adaptations and morphologies. They also demonstrate how EST-based nuclear resources can be used to more fully resolve the phylogenetic history of species radiations.