Identifying invertebrate invasions using morphological and molecular analyses: North American Daphnia ‘pulex’ in New Zealand fresh waters

We used a DNA barcoding approach to identify specimens of the Daphnia pulex complex occurring in New Zealand lakes, documenting the establishment of non-indigenous North American Daphnia 'pulex'. Morphological delineation of species in this complex is problematic due to a lack of good morphological traits to distinguish the species, as there is a relatively high degree of morphological stasis within the group through evolutionary time. Accordingly, genetic analyses were used to determine the specific identity and likely geographic origin of this species. Morphologically, individuals most closely resembled Daphnia pulicaria or Daphnia pulex sensu lato, which cannot be separated morphologically. Furthermore, each of these taxa comprises separate species in North America and Europe, despite carrying the same names. We identified individuals using a 658 bp nucleotide portion of the mitochondrial cytochrome c oxidase subunit 1 gene (COI) as North American Daphnia 'pulex', being distinct from European Daphnia pulex sensu stricto and D. pulicaria from Europe or North America. Cellulose allozyme electrophoresis was used to confirm that individuals were not hybrids with D. pulicaria. North American Daphnia 'pulex' in New Zealand were first recorded in New Zealand from South Island lakes that are popular for overseas recreational fishers, indicating a possible source of introduction for this species (e.g. on/in fishing gear). Our study provides an additional example of how genetic techniques can be used for the accurate identification of non-indigenous taxa, particularly when morphological species determination is not possible. The growth of global databases such as GenBank and Barcode of Life Datasystems (BOLD) will further enhance this identification capacity

Latitudinal distribution and mitochondrial DNA (COI) variability of Stereotydeus spp. (Acari: Prostigmata) in Victoria Land and the central Transantarctic Mountains

We examined mitochondrial DNA (COI) variability and distribution of Stereotydeus spp. in Victoria Land and the Transantarctic Mountains, and constructed Neighbour Joining (NJ) and Maximum Likelihood (ML) phylogenetic trees using all publicly available COI sequences for the three Stereotydeus species present (S. belli, S. mollis and S. shoupi). We also included new COI sequences from Miers, Marshall and Garwood valleys in southern Victoria Land (78°S), as well as from the Darwin (79°S) and Beardmore Glacier (83°S) regions. Both NJ and ML methods produced trees which were similar in topology differing only in the placement of the single available S. belli sequence from Cape Hallett (72°S) and a S. mollis haplotype from Miers Valley. Pairwise sequence divergences among species ranged from 9.5–18.1%. NJ and ML grouped S. shoupi from the Beardmore Glacier region as sister to those from the Darwin with pairwise divergences of 8%. These individuals formed a monophyletic clade with high bootstrap support basal to S. mollis and S. belli. Based on these new data, we suggest that the distributional range of S. shoupi extends northward to Darwin Glacier and that a barrier to dispersal for Stereotydeus, and possibly other arthropods, exists immediately to the north of this area

Phylogeography of New Zealand’s coastal benthos

During the past 30 years, 42 molecular studies have been undertaken in New Zealand to examine the phylogeography of coastal benthic invertebrates and plants. Here, we identify generalities and/or patterns that have emerged from this research and consider the processes implicated in generating genetic structure within populations. Studies have used various molecular markers and examined taxonomic groups with a range of life histories and dispersal strategies. Genetic disjunctions have been identified at multiple locations, with the most frequently observed division occurring between northern and southern populations at the top of the South Island. Although upwelling has been implicated as a cause of this disjunction, oceanographic evidence is lacking and alternative hypotheses exist. A significant negative correlation between larval duration and genetic differentiation (r2 = 0.39, P < 0.001, n = 29) across all studies suggests that larval duration might be used as a proxy for dispersal potential. However, among taxa with short larval durations (<10 days) there was greater variability in genetic differentiation than among taxa with longer pelagic periods. This variability implies that when larval duration is short, other factors may determine dispersal and connectivity among populations. Although there has been little congruence between the phylogeographic data and recognised biogeographic regions, recent research has resolved population subdivision at finer spatial scales corresponding more closely with existing biogeographic classifications. The use of fast-evolving and ecologically significant molecular markers in hypothesis-driven research could further improve our ability to detect population subdivision and identify the processes structuring marine ecosystems

Isolation and characterization of microsatellites in the lichen Buellia frigida (Physciaceae), an Antarctic endemic

Premise of the study: Microsatellite markers were characterized for an Antarctic endemic, Buellia frigida, to investigate population structure and origin of Antarctic lichens. Methods and Results: Five primer sets were characterized. All loci were polymorphic with eight to 16 alleles per locus in a sample of 59 lichens. Conclusions: The microsatellite markers potentially provide insight into population structure and gene flow of B. frigida

Biological identification of springtails (Hexapoda: Collembola) from the Canadian Arctic, using mitochondrial DNA barcodes

We evaluated sequence diversity in the mitochondrial cytochrome-c oxidase I (COI; EC 1.9.3.1) gene as a tool for resolving differences among species of Arctic springtails. The Collembola examined in this analysis were collected from Igloolik, Cornwallis, and Somerset islands and included representatives from all major families found in the Arctic. Members of 13 genera and 19 species were examined, including 4 species of the genus Folsomia and 3 species of the genus Hypogastrura. In all cases, species were successfully discriminated. Sequence divergences within species were generally less than 1%, whereas divergences between species were greater than 8% in all cases. Divergences among individuals of one species of Folsomia were much higher (up to 13%), but this likely represents the presence of an undescribed sibling species. We conclude that DNA barcoding is a powerful tool for identifying species of Collembola and should regularly be useful as a complement to traditional, morphological taxonomy

Constructing A Flexible Likelihood Function For Spectroscopic Inference

We present a modular, extensible likelihood framework for spectroscopic inference based on synthetic model spectra. The subtraction of an imperfect model from a continuously sampled spectrum introduces covariance between adjacent datapoints (pixels) into the residual spectrum. For the high signal-to-noise data with large spectral range that is commonly employed in stellar astrophysics, that covariant structure can lead to dramatically underestimated parameter uncertainties (and, in some cases, biases). We construct a likelihood function that accounts for the structure of the covariance matrix, utilizing the machinery of Gaussian process kernels. This framework specifically address the common problem of mismatches in model spectral line strengths (with respect to data) due to intrinsic model imperfections (e.g., in the atomic/molecular databases or opacity prescriptions) by developing a novel local covariance kernel formalism that identifies and self-consistently downweights pathological spectral line "outliers." By fitting many spectra in a hierarchical manner, these local kernels provide a mechanism to learn about and build data-driven corrections to synthetic spectral libraries. An open-source software implementation of this approach is available at http://iancze.github.io/Starfish, including a sophisticated probabilistic scheme for spectral interpolation when using model libraries that are sparsely sampled in the stellar parameters. We demonstrate some salient features of the framework by fitting the high resolution $V$-band spectrum of WASP-14, an F5 dwarf with a transiting exoplanet, and the moderate resolution $K$-band spectrum of Gliese 51, an M5 field dwarf.Comment: Accepted to ApJ. Incorporated referees' comments. New figures 1, 8, 10, 12, and 14. Supplemental website: http://iancze.github.io/Starfish

Testing use of mitochondrial COI sequences for the identification and phylogenetic analysis of New Zealand caddisflies (Trichoptera)

We tested the hypothesis that cytochrome c oxidase subunit 1 (COI) sequences would successfully discriminate recognised species of New Zealand caddisflies. We further examined whether phylogenetic analyses, based on the COI locus, could recover currently recognised superfamilies and suborders. COI sequences were obtained from 105 individuals representing 61 species and all 16 families of Trichoptera known from New Zealand. No sequence sharing was observed between members of different species, and congeneric species showed from 2.3 to 19.5% divergence. Sequence divergence among members of a species was typically low (mean = 0.7%; range 0.0–8.5%), but two species showed intraspecific divergences in excess of 2%. Phylogenetic reconstructions based on COI were largely congruent with previous conclusions based on morphology, although the sequence data did not support placement of the purse-cased caddisflies (Hydroptilidae) within the uncased caddisflies, and, in particular, the Rhyacophiloidea. We conclude that sequence variation in the COI gene locus is an effective tool for the identification of New Zealand caddisfly species, and can provide preliminary phylogenetic inferences. Further research is needed to ascertain the significance of the few instances of high intra-specific divergence and to determine if any instances of sequence sharing will be detected with larger sample sizes

Lake Area Variability Across a Climatic and Vegetational Transect in Southeastern Alberta

Areas of 34 small lakes forming a transect across the southern margin of the Boreal Forest into the Grassland in southern Alberta were obtained from 326 aerial photographs, with at least six photographs for each lake in different months and different years from 1949 to 1992. Standard deviations of standardised lake areas (used as an index of lake area sensitivity to short term climate fluctuations) were plotted against a climatic moisture index; the resulting scatter of points is constrained by a function relating lake sensitivity to long-term regional climatic moisture. The lakes show high sensitivity in the Grassland where potential évapotranspiration exceeds precipitation, a steep drop in sensitivity over a small range of climatic moisture values in the Aspen Parkland, and very low sensitivity in the Boreal Forest where precipitation exceeds potential évapotranspiration.Les superficies de 34 petits lacs constituant un transect à partir de la limite méridionale de la forêt boréale jusqu'à la prairie, dans le sud de l'Alberta. ont été calculées grâce à l'étude de 326 photographies aériennes. Chacun des lacs comptaient au moins six photographies prises à différents mois et échelonnées de 1949 à 1992. Les écarts types de la superficie standardisée des lacs (employés comme indice de la sensibilité de la superficie des lacs aux fluctuations climatiques à court terme) ont été reportés par rapport à l'indice d'humidité. Le nuage de points qui en résulte est commandé par la fonction reliant la sensibilité des lacs à l'humidité du climat régional. Les lacs démontrent une grande sensibilité en prairie où l'évapotranspiration potentielle excède les précipitations, une très forte baisse de sensibilité dans la tremblaie-parc et une très faible sensibilité dans la forêt boréale où les précipitations excèdent l'évapotranspiration potentielle.Die Ausdehnungen von 34 kleinen Seen, welche ein Transect von der sùdlichen Grenze des nôrdlichen Waldgùrtels bis zur Prârie bilden, wurden mittels 326 Luftaufnahmen berechnet; dabei hat man mindestens sechs Aufnahmen fur jeden See gemacht, in verschiedenen Monaten und verschiedenen Jahren von 1949 bis 1992. Die Standardabweichungen von den standardisierten Seen-Oberflàchen (welche als Gradmesser fur die Sensibilitàt der Seen-Oberflâchen auf kurzfristige klimatische Schwankungen benutzt wurden) hat man in Bezug auf den klimatischen Feuchtigkeitsindex ubertragen: die hierdurch erzielte Streuung von Punkten ist durch die Funktion bestimmt, welche die Seen-Sensibilitât mit langzeitiger regionaler klimatischer Feuchtigkeit verbindet. Die Seen weisen eine hohe Sensibilitàt in der Prârie auf, wo die potentielle Evapotranspiration die Niederschlàge ùbertrifft, eine jâhe Abnahme der Sensibilitàt ùber einer kleinen Reihe von klimatischen Feuchtig-keitswerten im Aspen Parkland, und sehr niedrige Sensibilitàt im nôrdlichen WaIdgùrtel, wo die Niederschlàge hoher als die potentielle Evapotranspiration sind