The island-scale internal wave climate of Moorea, French Polynesia

Analysis of five-year records of temperatures and currents collected at Moorea reveal strong internal wave activity at predominantly semi-diurnal frequencies impacting reef slopes at depths 30m around the entire island. Temperature changes of 1.5C to 3C are accompanied by surges of upward and onshore flow and vertical shear in onshore currents. Superimposed on annual temperature changes of approximately 3C, internal wave activity is high from Oct-May and markedly lower from Jun-Sep. The offshore pycnocline is broadly distributed with continuous stratification to at least 500m depth, and a subsurface fluorescence maximum above the strong nutricline at approximately 200m. Minimum buoyancy periods range from 4.8 to 6min, with the maximum density gradient occurring at 50 to 60m depth in summer and deepening to approximately 150 to 200m in winter. The bottom slope angle around all of Moorea is super-critical relative to the vertical stratification angle suggesting that energy propagating into shallow water is only a portion of total incident internal wave energy. Vertical gradient Richardson numbers indicate dominance by density stability relative to current shear with relatively limited diapycnal mixing. Coherence and lagged cross-correlation of semi-diurnal temperature variation indicate complex patterns of inter-site arrival of internal waves and no clear coherence or lagged correlation relationships among island sides. Semi-diurnal and high frequency internal wave packets likely arrive on Moorea from a combination of local and distant sources and may have important impacts for nutrient and particle fluxes in deep reef environments. © 2012 American Geophysical Union. All Rights Reserved.

Biogeography in deep time - What do phylogenetics, geology, and paleoclimate tell us about early platyrrhine evolution?

Molecular data have converged on a consensus about the genus-level phylogeny of extant platyrrhine monkeys, but for most extinct taxa and certainly for those older than the Pleistocene we must rely upon morphological evidence from fossils. This raises the question as to how well anatomical data mirror molecular phylogenies and how best to deal with discrepancies between the molecular and morphological data as we seek to extend our phylogenies to the placement of fossil taxa. Here I present parsimony-based phylogenetic analyses of extant and fossil platyrrhines based on an anatomical dataset of 399 dental characters and osteological features of the cranium and postcranium. I sample 16 extant taxa (one from each platyrrhine genus) and 20 extinct taxa of platyrrhines. The tree structure is constrained with a "molecular scaffold" of extant species as implemented in maximum parsimony using PAUP with the molecular-based 'backbone' approach. The data set encompasses most of the known extinct species of platyrrhines, ranging in age from latest Oligocene (∼26 Ma) to the Recent. The tree is rooted with extant catarrhines, and Late Eocene and Early Oligocene African anthropoids. Among the more interesting patterns to emerge are: (1) known early platyrrhines from the Late Oligocene through Early Miocene (26-16.5Ma) represent only stem platyrrhine taxa; (2) representatives of the three living platyrrhine families first occur between 15.7 Ma and 13.5 Ma; and (3) recently extinct primates from the Greater Antilles (Cuba, Jamaica, Hispaniola) are sister to the clade of extant platyrrhines and may have diverged in the Early Miocene. It is probable that the crown platyrrhine clade did not originate before about 20-24 Ma, a conclusion consistent with the phylogenetic analysis of fossil taxa presented here and with recent molecular clock estimates. The following biogeographic scenario is consistent with the phylogenetic findings and climatic and geologic evidence: Tropical South America has been a center for platyrrhine diversification since platyrrhines arrived on the continent in the middle Cenozoic. Platyrrhines dispersed from tropical South America to Patagonia at ∼25-24 Ma via a "Paraná Portal" through eastern South America across a retreating Paranense Sea. Phylogenetic bracketing suggests Antillean primates arrived via a sweepstakes route or island chain from northern South America in the Early Miocene, not via a proposed land bridge or island chain (GAARlandia) in the Early Oligocene (∼34 Ma). Patagonian and Antillean platyrrhines went extinct without leaving living descendants, the former at the end of the Early Miocene and the latter within the past six thousand years. Molecular evidence suggests crown platyrrhines arrived in Central America by crossing an intermittent connection through the Isthmus of Panama at or after 3.5Ma. Any more ancient Central American primates, should they be discovered, are unlikely to have given rise to the extant Central American taxa in situ.

Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates.

Dopamine is an important central nervous system transmitter that functions through two classes of receptors (D1 and D2) to influence a diverse range of biological processes in vertebrates. With roles in regulating neural activity, behavior, and gene expression, there has been great interest in understanding the function and evolution dopamine and its receptors. In this study, we use a combination of sequence analyses, microsynteny analyses, and phylogenetic relationships to identify and characterize both the D1 (DRD1A, DRD1B, DRD1C, and DRD1E) and D2 (DRD2, DRD3, and DRD4) dopamine receptor gene families in 43 recently sequenced bird genomes representing the major ordinal lineages across the avian family tree. We show that the common ancestor of all birds possessed at least seven D1 and D2 receptors, followed by subsequent independent losses in some lineages of modern birds. Through comparisons with other vertebrate and invertebrate species we show that two of the D1 receptors, DRD1A and DRD1B, and two of the D2 receptors, DRD2 and DRD3, originated from a whole genome duplication event early in the vertebrate lineage, providing the first conclusive evidence of the origin of these highly conserved receptors. Our findings provide insight into the evolutionary development of an important modulatory component of the central nervous system in vertebrates, and will help further unravel the complex evolutionary and functional relationships among dopamine receptors.

Response to Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds".

Mitchell et al. argue that divergence-time estimates for our avian phylogeny were too young because of an "inappropriate" maximum age constraint for the most recent common ancestor of modern birds and that, as a result, most modern bird orders diverged before the Cretaceous-Paleogene mass extinction event 66 million years ago instead of after. However, their interpretations of the fossil record and timetrees are incorrect.

Tree species-area and species-diameter relationships at three lowland rain forest sites in Sumatra

Data from three forest sites in Sumatra (Batang Ule, Pasirmayang and Tebopandak) have been analysed and compared for the effects of sample area cut-off, and tree diameter cut-off. An 'extended inverted exponential model' is shown to be well suited to fitting tree-species-area curves. The model yields species carrying capacities of 680 for Batang Ule, 380 species for Pasirmayang, and 35 for Tebopandak (tree diameter >10cm). It would seem that in terms of species carrying capacity, Tebopandak and Pasirmayang are rather similar, and both less diverse than the hilly Batang Ule site. In terms of conservation policy, this would mean that rather more emphasis should be put on conserving hilly sites on a granite substratum. For Pasirmayang with tree diameter >3cm, the asymptotic species number estimate is 567, considerably higher than the estimate of 387 species for trees with diameter >10cm. It is clear that the diameter cut-off has a major impact on the estimate of the species carrying capacity. A conservative estimate of the total number of tree species in the Pasirmayang region is 632 species! In sampling exercises, the diameter cut-off should not be chosen lightly, and it may be worth adopting field sampling procedures which involve some subsampling of the primary sample area, where the diameter cut-off is set much lower than in the primary plots.

A new parameterization of Johnson's SB distribution with application to fitting forest tree diameter data

The SB distributional model of Johnson's 1949 paper was introduced by a transformation to normality, that is, z ~ N(0, 1), consisting of a linear scaling to the range (0, 1), a logit transformation, and an affine transformation, z = γ + δu. The model, in its original parameterization, has often been used in forest diameter distribution modelling. In this paper, we define the SB distribution in terms of the inverse transformation from normality, including an initial linear scaling transformation, u = γ′ + δ′z (δ′ = 1/δ and γ′ = �γ/δ). The SB model in terms of the new parameterization is derived, and maximum likelihood estimation schema are presented for both model parameterizations. The statistical properties of the two alternative parameterizations are compared empirically on 20 data sets of diameter distributions of Changbai larch (Larix olgensis Henry). The new parameterization is shown to be statistically better than Johnson's original parameterization for the data sets considered here.

Tree diameter distribution modelling: introducing the logitlogistic distribution

Johnson's SB distribution is a four-parameter distribution that is transformed into a normal distribution by a logit transformation. By replacing the normal distribution of Johnson's SB with the logistic distribution, we obtain a new distributional model that approximates SB. It is analytically tractable, and we name it the "logitlogistic" (LL) distribution. A generalized four-parameter Weibull model and the Burr XII model are also introduced for comparison purposes. Using the distribution "shape plane" (with axes skew and kurtosis) we compare the "coverage" properties of the LL, the generalized Weibull, and the Burr XII with Johnson's SB, the beta, and the three-parameter Weibull, the main distributions used in forest modelling. The LL is found to have the largest range of shapes. An empirical case study of the distributional models is conducted on 107 sample plots of Chinese fir. The LL performs best among the four-parameter models.

Bivariate distribution modeling with tree diameter and height data

The Logit-Logistic (LL), Johnson's SB, and the Beta (GBD) are flexible four-parameter probability distribution models in terms of the (skewness-kurtosis) region covered, and each has been used for modeling tree diameter distributions in forest stands. This article compares bivariate forms of these models in terms of their adequacy in representing empirical diameter-height distributions from 102 sample plots. Four bivariate models are compared: SBB, the natural, well-known, and much-used bivariate generalization of SB; the bivariate distributions with LL, SB, and Beta as marginals, constructed using Plackett's method (LL-2P, etc.). All models are fitted using maximum likelihood, and their goodness-of-fits are compared using minus log-likelihood (equivalent to Akaike's Information Criterion, the AIC). The performance ranking in this case study was SBB, LL-2P, GBD-2P, and SB-2P

A new species of Tortanus (Atortus)(Copepoda: Calanoida: Tortanidae) from Rodrigues Island, Mauritius

A new species of the copepod genus Tortanus (Atortus) (Copepoda: Calanoida), T. (A.) insularis, is described from the coastal region of Rodrigues Island, Mauritius, an isolated island in the south-western Indian Ocean. This new species can be assigned to an Indian element, the recticauda species group, in the Indo-West Pacific recticauda species complex. It exhibits the closest relationship to T. (A.) recticauda recorded from the southern Red Sea and Arabian Gulf, rather than the more closely distributed T. (A.) capensis, recorded from off South Africa.

A new procedure to optimize the selection of groups in a classification tree

Agglomerative cluster analyses encompass many techniques, which have been widely used in various fields of science. In biology, and specifically ecology, datasets are generally highly variable and may contain outliers, which increase the difficulty to identify the number of clusters. Here we present a new criterion to determine statistically the optimal level of partition in a classification tree. The criterion robustness is tested against perturbated data (outliers) using an observation or variable with values randomly generated. The technique, called Random Simulation Test (RST), is tested on (1) the well-known Iris dataset [Fisher, R.A., 1936. The use of multiple measurements in taxonomic problems. Ann. Eugenic. 7, 179–188], (2) simulated data with predetermined numbers of clusters following Milligan and Cooper [Milligan, G.W., Cooper, M.C., 1985. An examination of procedures for determining the number of clusters in a data set. Psychometrika 50, 159–179] and finally (3) is applied on real copepod communities data previously analyzed in Beaugrand et al. [Beaugrand, G., Ibanez, F., Lindley, J.A., Reid, P.C., 2002. Diversity of calanoid copepods in the North Atlantic and adjacent seas: species associations and biogeography. Mar. Ecol. Prog. Ser. 232, 179–195]. The technique is compared to several standard techniques. RST performed generally better than existing algorithms on simulated data and proved to be especially efficient with highly variable datasets.

Island-coastal and oceanic epipelagic zooplankton biodiversity in the southwestern Indian Ocean

The oceanic Indian Ocean zooplankton species and their distributions have been well described, but the zooplankton of coastal regions, particularly around the oceanic islands, has not been well researched, either taxonomically or experimentally. The environment of the Mascarene region in the southwestern Indian Ocean and zooplankton research that has been carried out there is detailed, along with gaps in our knowledge. Suggestions are given for future research, particularly on the zooplankton species adapted to live in the fluctuating environment of inshore waters, including studies on taxonomy and biodiversity, life cycles, dispersion and genetics. Problems of carrying out taxonomic research are highlighted.