[show abstract][hide abstract] ABSTRACT: We report three new avian mitochondrial genomes, two from widely separated groups of owls, and a falcon relative (the Secretarybird). We then report additional progress in resolving Neoavian relationships in that the two groups of owls do come together (it is not just long-branch attraction), and the Secretarybird is the deepest divergence on the Accipitridae lineage. This is now agreed between mitochondrial and nuclear sequences. There is no evidence for the monophyly of the combined three groups of raptors (owls, eagles and falcons), and again this is agreed by nuclear and mitochondrial sequences. All three groups (owls, accipitrids (eagles) and falcons) do appear to be members of the 'higher land birds', and though there may not yet be full 'consilience' between mitochondrial and nuclear sequences for the precise order of divergences of the eagles, falcons and the owls, there is good progress on their relationships.
Genome Biology and Evolution 01/2014; · 4.76 Impact Factor
[show abstract][hide abstract] ABSTRACT: Predicting survival and extinction scenarios for climate change requires an understanding of the present day ecological characteristics of species and future available habitats, but also the adaptive potential of species to cope with environmental change. Hybridization is one mechanism that could facilitate this. Here we report statistical evidence that the transfer of genetic information through hybridization is a feature of species from the plant genus Pachycladon that survived the Last Glacial Maximum in geographically separated alpine refugia in New Zealand’s South Island. We show that transferred glucosinolate hydrolysis genes also exhibit evidence of intra-locus recombination. Such gene exchange and recombination has the potential to alter the chemical defence in the offspring of hybridizing species. We use a mathematical model to show that when hybridization increases the adaptive potential of species, future biodiversity will be best protected by preserving closely related species that hybridize rather than by conserving distantly related species that are genetically isolated.
[show abstract][hide abstract] ABSTRACT: The phylogenetic branching order of the green algal groups that gave rise to land plants remains uncertain despite its fundamental importance to understanding plant evolution. Previous studies have demonstrated that land plants evolved from streptophyte algae, but different lineages of streptophytes have been suggested to be the sister group of land plants. To better understand the evolutionary history of land plants, and to determine the potential effects of "long-branch attraction" in phylogenetic reconstruction, we analysed a chloroplast genome dataset including three new chloroplast genomes from streptophyte algae: Coleochaetae orbicularis (Coleochaetales), Nitella hookeri (Charales), and Spirogyra communis (Zygnematales). We further applied a site pattern sorting method together with site- and time-heterogeneous models to investigate the branching order among streptophytes and land plants. Our chloroplast phylogenomic analyses support previous hypotheses based on nuclear data in placing Zygnematales alone, or a clade consisting of Coleochaetales plus Zygnematales, as the closest living relatives of land plants.
Molecular Biology and Evolution 10/2013; · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: Recently, we reported the chloroplast genome-wide association of oligonucleotide repeats, indels and nucleotide substitutions in aroid chloroplast genomes. We hypothesized that the distribution of oligonucleotide repeat sequences in a single representative genome can be used to identify mutational hotspots and loci suitable for population genetic, phylogenetic and phylogeographic studies. Using information on the location of oligonucleotide repeats in the chloroplast genome of taro (Colocasia esculenta), we designed 30 primer pairs to amplify and sequence polymorphic loci. The primers have been tested in a range of intra-specific to intergeneric comparisons, including ten taro samples (Colocasia esculenta) from diverse geographical locations, four other Colocasia species (C. affinis, C. fallax, C. formosana, C. gigantea) and three other aroid genera (represented by Remusatia vivipara, Alocasia brisbanensis and Amorphophallus konjac). Multiple sequence alignments for the intra-specific comparison revealed nucleotide substitutions (point mutations) at all 30 loci and microsatellite polymorphisms at 14 loci. The primer pairs reported here reveal levels of genetic variation suitable for high-resolution phylogeographic and evolutionary studies of taro and other closely related aroids. Our results confirm that information on repeat distribution can be used to identify loci suitable for such studies, and we expect that this approach can be used in other plant groups.
[show abstract][hide abstract] ABSTRACT: There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward.
Briefings in Bioinformatics 05/2013; · 5.30 Impact Factor
[show abstract][hide abstract] ABSTRACT: Here we investigate the diversity of pathogenic Vibrio species in marine environments close to Suva, Fiji. We use four distinct yet complementary analyses - biochemical testing, phylogenetic analyses, metagenomic analyses and molecular typing - to provide some preliminary insights into the diversity of vibrios in this region. Taken together our analyses confirmed the presence of nine Vibrio species, including three of the most important disease-causing vibrios (i.e. V. cholerae, V. parahaemolyticus and V. vulnificus), in Fijian marine environments. Furthermore, since toxigenic V. parahaemolyticus are present on fish for consumption we suggest these bacteria represent a potential public health risk. Our results from Illumina short read sequencing are encouraging in the context of microbial profiling and biomonitoring. They suggest this approach may offer an efficient and cost-effective method for studying the dynamics of microbial diversity in marine environments over time.
[show abstract][hide abstract] ABSTRACT: Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the 'Melanesian' contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.
PLoS ONE 01/2012; 7(12):e52022. · 3.73 Impact Factor
[show abstract][hide abstract] ABSTRACT: A thriving population of the Indian brown mongoose (Herpestes fuscus), native to southwest India and Sri Lanka, has been discovered on the island of Viti Levu in Fiji. This is the first known
introduction of this species and may derive from a pair brought from an unknown source to a private zoo in the late 1970s.
They co-occur on Viti Levu with the much smaller small Indian mongoose (H. auropunctatus), and they are probably nocturnally active. No research has been conducted on their activity, diet, or impact on Fiji.
[show abstract][hide abstract] ABSTRACT: Abstract Background The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level. Results Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades. Conclusions Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats.
[show abstract][hide abstract] ABSTRACT: Until now, phylogenetic studies of the mongooses (Carnivora, Herpestidae) have not included an exhaustive sampling of the Asian members of this family. In this study, we used mitochondrial (Cytochrome b and ND2), nuclear (beta-fibrinogen intron 7 and Transthyretin intron 1) sequences from almost all of the recognized mongoose species to produce a well-resolved phylogeny of the Herpestidae. We also performed molecular dating analyses to infer divergence dates of the different lineages within the Herpestidae. Our results confirmed the paraphyly of the Herpestes genus and other phylogenetic relationships, which previously had only been moderately supported. The Asian herpestid species were found to form a monophyletic group within the Herpestidae. Within the Asian species, a cyto-nuclear conflict was discovered between the small Indian mongoose (Herpestes auropunctatus), the Indian gray mongoose (Herpestes edwardsii) and the Javan mongoose (Herpestes javanicus), which may have occurred through interspecific hybridization. This study inferred an Early Miocene origin for the Herpestidae and a Middle Miocene origin for the Asian mongooses.
Molecular Phylogenetics and Evolution 07/2009; 53(1):69-80. · 4.07 Impact Factor
[show abstract][hide abstract] ABSTRACT: The extent and evolutionary significance of hybridization is difficult to evaluate because of the difficulty in distinguishing hybridization from incomplete lineage sorting. Here we present a novel parametric approach for statistically distinguishing hybridization from incomplete lineage sorting based on minimum genetic distances of a nonrecombining locus. It is based on the idea that the expected minimum genetic distance between sequences from two species is smaller for some hybridization events than for incomplete lineage sorting scenarios. When applied to empirical data sets, distributions can be generated for the minimum interspecies distances expected under incomplete lineage sorting using coalescent simulations. If the observed distance between sequences from two species is smaller than its predicted distribution, incomplete lineage sorting can be rejected and hybridization inferred. We demonstrate the power of the method using simulations and illustrate its application on New Zealand alpine buttercups (Ranunculus). The method is robust and complements existing approaches. Thus it should allow biologists to assess with greater accuracy the importance of hybridization in evolution.
The American Naturalist 07/2009; 174(2):E54-70. · 4.55 Impact Factor
[show abstract][hide abstract] ABSTRACT: The timing and order of divergences within the genus Rattus have, to date, been quite speculative. In order to address these important issues we sequenced six new whole mitochondrial genomes from wild-caught specimens from four species, Rattus exulans, Rattus praetor, Rattus rattus and Rattus tanezumi. The only rat whole mitochondrial genomes available previously were all from Rattus norvegicus specimens. Our phylogenetic and dating analyses place the deepest divergence within Rattus at approximately 3.5 million years ago (Mya). This divergence separates the New Guinean endemic R. praetor lineage from the Asian lineages. Within the Asian/Island Southeast Asian clade R. norvegicus diverged earliest at approximately 2.9Mya. R. exulans and the ancestor of the sister species R. rattus and R. tanezumi subsequently diverged at approximately 2.2Mya, with R. rattus and R. tanezumi separating as recently as approximately 0.4Mya. Our results give both a better resolved species divergence order and diversification dates within Rattus than previous studies.
Molecular Phylogenetics and Evolution 09/2008; 49(2):460-6. · 4.07 Impact Factor
[show abstract][hide abstract] ABSTRACT: Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade.
Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the beta-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes). Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved.
Our phylogenetic hypothesis based on 41 avian mitochondrial genomes (13,229 bp) rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves.
[show abstract][hide abstract] ABSTRACT: Incomplete taxon sampling has been a major problem in resolving the early divergences in birds. Five new mitochondrial genomes are reported here (brush-turkey, lyrebird, suboscine flycatcher, turkey vulture, and a gull) and three break up long branches that tended to attract the distant reptilian outgroup. These long branches were to galliforms, and to oscine and suboscine passeriformes. Breaking these long branches leaves the root, as inferred by maximum likelihood and Bayesian phylogenetic analyses, between paleognaths and neognaths. This means that morphological, nuclear, and mitochondrial data are now in agreement on the position of the root of the avian tree and we can, move on to other questions. An overview is then given of the deepest divisions in the mitogenomic tree inferred from complete mitochondrial genomes. The strict monophyly of both the galloanseres and the passerines is strongly supported, leaving the deep six-way split within Neoaves as the next major question for which resolution is still lacking. Incomplete taxon sampling was also a problem for Neoaves, and although some resolution is now available there are still problems because current phylogenetic methods still fail to account for real features of DNA sequence evolution.
Molecular Phylogenetics and Evolution 02/2007; 42(1):1-13. · 4.07 Impact Factor
[show abstract][hide abstract] ABSTRACT: The South Island, New Zealand, endemics Lepidium sisymbrioides and L. solandri are accepted at species rank. L. solandri Kirk is reinstated and includes L. matau Petrie in synonymy, and L. kawarau is reduced to synonymy of L. sisymbrioides. Twenty‐nine floral and vegetative morphological characters were measured and used for analyses of character variation and principal components analysis. Leaf characters proved to be the most useful in distinguishing between L. sisymbrioides and L. solandri, with 12 of the 15 leaf characters having significantly different means. Only 7 of the 14 floral characters included in the study have significantly different means. In comparison to L. solandri, L. sisymbrioides has longer and narrower terminal and primary pinnae and cauline leaves, more secondary pinnae and cauline leaf lobes, less hairy sepals and ovaries, narrower ovaries, and shorter filaments. L. sisymbrioides occurs on rock outcrops in the upper Manuherikia, Waitaki, and Kawarau river valleys. L. solandri grows mainly on alluvium and outwash gravels in semi‐arid parts of inland Canterbury and Central Otago.DNA sequence data from ITS, ETS, and trnL‐trnF markers were used to examine phylogenetic patterns in L. sisymbrioides and L. solandri, and the related species L. kirkii, L. naufragorum, and L. tenuicaule. There is substantial variation in these markers in L. sisymbrioides and L. solandri, and this is considered to be due to introgression from other species of Lepidium, such as L. kirkii and L. tenuicaule. Much of the variation in the ETS sequences occurs in samples of L. sisymbrioides and L. solandri from the Manuherikia River valley, and this can be attributed to geneflow with the sympatric L. kirkii.Lepidium sisymbrioides and L. solandri are considered to be “Acutely Threatened, Nationally Endangered” using the New Zealand threatened plant classification criteria. In this assessment both species are considered to be data poor. Further field survey for new populations is required.
New Zealand Journal of Botany 01/2007; 45:237-264. · 0.62 Impact Factor
[show abstract][hide abstract] ABSTRACT: Laccopetalum giganteum (Ranunculaceae) is a rare endemic buttercup from the montane regions of the Peruvian Andes. The systematic position of this
monotypic genus within Ranunculaceae was investigated using cpDNA matK sequence data. Our findings indicate that L. giganteum forms a highly supported clade together with Krapfia. Several morphological characters are shared by these genera; large subglobose and fleshy flowers, presence of androgynophore
with a separated staminal and carpellate region and many tiny achenes. The Laccopetalum-Krapfia clade is sister to the core Ranunculus group with a high bootstrap support. The number of sepals and similar characteristics of achene morphology support an affinity
of Laccopetalum with Ranunculus s.s tr.
Plant Systematics and Evolution 01/2007; 264(1):109-116. · 1.31 Impact Factor
[show abstract][hide abstract] ABSTRACT: The origin of the Polynesian bottle gourd (Lagenaria siceraria), an important crop species in prehistoric Polynesia, has remained elusive. Most recently, a South American origin has been favored as the bottle gourd could have been introduced from this continent with the sweet potato by Polynesian voyagers around A.D. 1,000. To test the hypothesis of an American origin for the Polynesian bottle gourd, we developed seven markers specific to bottle gourd (two chloroplast and five nuclear). The nuclear markers were developed using a new technique where polymorphic inter simple sequence repeat (ISSR) markers are converted into single-locus polymerase chain reaction and sequencing markers--an approach that will be useful for developing markers in other taxa. All seven markers were sequenced in 36 cultivars of bottle gourd from Asia, the Americas, and Polynesia. The results support a dual origin for the Polynesian bottle gourd: the chloroplast markers are exclusively of Asian origin, but the nuclear markers show alleles originating in both the Americas and Asia. Because hybridization of Polynesian bottle gourds with post-European introductions cannot be excluded, ancient DNA from archaeological material will be useful for further elucidating the prehistoric movements of this species in Polynesia. This work has implications not only for the dispersal of the Polynesian bottle gourd but also for the domestication and dispersal of the species as a whole.
Molecular Biology and Evolution 06/2006; 23(5):893-900. · 10.35 Impact Factor
[show abstract][hide abstract] ABSTRACT: Australasian marsupials include three major radiations, the insectivorous/carnivorous Dasyuromorphia, the omnivorous bandicoots (Peramelemorphia), and the largely herbivorous diprotodontians. Morphologists have generally considered the bandicoots and diprotodontians to be closely related, most prominently because they are both syndactylous (with the 2nd and 3rd pedal digits being fused). Molecular studies have been unable to confirm or reject this Syndactyla hypothesis. Here we present new mitochondrial (mt) genomes from a spiny bandicoot (Echymipera rufescens) and two dasyurids, a fat-tailed dunnart (Sminthopsis crassicaudata) and a northern quoll (Dasyurus hallucatus). By comparing trees derived from pairwise base-frequency differences between taxa with standard (absolute, uncorrected) distance trees, we infer that composition bias among mt protein-coding and RNA sequences is sufficient to mislead tree reconstruction. This can explain incongruence between trees obtained from mt and nuclear data sets. However, after excluding major sources of compositional heterogeneity, both the "reduced-bias" mt and nuclear data sets clearly favor a bandicoot plus dasyuromorphian association, as well as a grouping of kangaroos and possums (Phalangeriformes) among diprotodontians. Notably, alternatives to these groupings could only be confidently rejected by combining the mt and nuclear data. Elsewhere on the tree, Dromiciops appears to be sister to the monophyletic Australasian marsupials, whereas the placement of the marsupial mole (Notoryctes) remains problematic. More generally, we contend that it is desirable to combine mt genome and nuclear sequences for inferring vertebrate phylogeny, but as separately modeled process partitions. This strategy depends on detecting and excluding (or accounting for) major sources of non-historical signal, such as from compositional non-stationarity. [Base composition; combined data; marsupial; mitochondrial genome; phylogeny.].
[show abstract][hide abstract] ABSTRACT: Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anseranas semipalmata), an owl (morepork, Ninox novaeseelandiae); a basal passerine (rifleman, or New Zealand wren, Acanthisitta chloris); and a parrot (kakapo or owl-parrot, Strigops habroptilus). The magpie goose provides an important new calibration point for avian evolution because the well-studied Presbyornis fossils are on the lineage to ducks and geese, after the separation of the magpie goose. We find, as with other animal mitochondrial genomes, that RY-coding is helpful in adjusting for biases between pyrimidines and between purines. When RY-coding is used at third positions of the codon, the root occurs between paleognath and neognath birds (as expected from morphological and nuclear data). In addition, passerines form a relatively old group in Neoaves, and many modern avian lineages diverged during the Cretaceous. Although many aspects of the avian tree are stable, additional taxon sampling is required.
Molecular Biology and Evolution 07/2004; 21(6):974-83. · 10.35 Impact Factor