Contemporary genetic, historical genetic and morphological data sets for the Yellow-tufted Honeyeater Lichenostomus melanops

Understanding the evolutionary history of threatened populations can improve their conservation management. Re-establishment of past but recent gene flow could re-invigorate threatened populations and replenish genetic diversity, necessary for population persistence. One of the four nominal subspecies of the common yellow-tufted honeyeater, Lichenostomus melanops cassidix, is critically endangered despite substantial conservation efforts over 55 years. Using a combination of morphometric, genetic and modelling approaches we tested for its evolutionary distinctiveness and conservation merit. We confirmed that cassidix has at least one morphometric distinction. It also differs genetically from the other subspecies in allele frequencies but not phylogenetically, implying that its evolution was recent. Modelling historical distribution supported the lack of vicariance and suggested a possibility of gene flow among subspecies at least since the late Pleistocene. Multi-locus coalescent analyses indicated that cassidix diverged from its common ancestor with neighbouring subspecies gippslandicus sometime from the mid-Pleistocene to the Holocene, and that it has the smallest historical effective population size of all subspecies. It appears that cassidix diverged from its ancestor with gippslandicus through a combination of drift and local selection. From patterns of genetic subdivision on two spatial scales and morphological variation we concluded that cassidix, gippslandicus and (melanops + meltoni) are diagnosable as subspecies. Low genetic diversity and effective population size of cassidix may translate to low genetic fitness and evolutionary potential, thus managed gene flow from gippslandicus is recommended for its recovery.

Seawater carbonate chemistry and early development of the sea urchin Lytechinus variegatus in a laboratory experiment using artificial seawater

Land-based aquaculture facilities often utilize additional bicarbonate sources such as commercial sea salts that are designed to boost alkalinity in order to buffer seawater against reductions in pH. Despite these preventative measures, many facilities are likely to face occasional reductions in pH and corresponding reductions in carbonate saturation states due to the accumulation of metabolic waste products. We investigated the impact of reduced carbonate saturation states (Omega Ca, Omega Ar) on embryonic developmental rates, larval developmental rates, and echinoplutei skeletal morphometrics in the common edible sea urchin Lytechinus variegatus under high alkalinity conditions. Commercial artificial seawater was bubbled with a mixture of air and CO2 gas to reduce the carbonate saturation state. Rates of embryonic and larval development were significantly delayed in both the low and extreme low carbonate saturation state groups relative to the control at a given time. Although symmetry of overall skeletal body lengths was not affected, allometric relationships were significantly different between treatment groups. Larvae reared under ambient conditions had significantly greater postoral arm and overall body lengths relative to body lengths than larvae grown under extreme low carbonate saturation state conditions, indicating that extreme changes in the carbonate system affected not only developmental rates but also larval skeletal shape. Reduced rates of embryonic development and delayed and altered larval skeletal growth are likely to negatively impact larval culturing of L. variegatus in land-based, intensive culture situations where calcite and aragonite saturation states are lowered by the accumulation of metabolic waste products.

Seawater carbonate chemistry, mortality and hatching rate, size and mass of Clupea harengus during experiments, 2011

Due to atmospheric accumulation of anthropogenic CO2 the partial pressure of carbon dioxide (pCO2) in surface seawater increases and the pH decreases. This process known as ocean acidification might have severe effects on marine organisms and ecosystems. The present study addresses the effect of ocean acidification on early developmental stages, the most sensitive stages in life history, of the Atlantic herring (Clupea harengus L.). Eggs of the Atlantic herring were fertilized and incubated in artificially acidified seawater (pCO2 1260, 1859, 2626, 2903, 4635 µatm) and a control treatment (pCO2 480 µatm) until the main hatch of herring larvae occurred. The development of the embryos was monitored daily and newly hatched larvae were sampled to analyze their morphometrics, and their condition by measuring the RNA/DNA ratios. Elevated pCO2 neither affected the embryogenesis nor the hatch rate. Furthermore the results showed no linear relationship betweenpCO2 and total length, dry weight, yolk sac area and otolith area of the newly hatched larvae. For pCO2 and RNA/DNA ratio, however, a significant negative linear relationship was found. The RNA concentration at hatching was reduced at higher pCO2 levels, which could lead to a decreased protein biosynthesis. The results indicate that an increased pCO2 can affect the metabolism of herring embryos negatively. Accordingly, further somatic growth of the larvae could be reduced. This can have consequences for the larval fish, since smaller and slow growing individuals have a lower survival potential due to lower feeding success and increased predation mortality. The regulatory mechanisms necessary to compensate for effects of hypercapnia could therefore lead to lower larval survival. Since the recruitment of fish seems to be determined during the early life stages, future research on the factors influencing these stages are of great importance in fisheries science.

Biología reproductiva de Polioptila lembeyei (Aves: Polioptilidae) en la Reserva Ecológica Siboney-Juticí, Santiago de Cuba, Cuba

Se estudió la biología reproductiva de Polioptila lembeyei en la Reserva Ecológica Siboney-Juticí, Santiago de Cuba, Cuba durante los años 2006 y 2007 en seis formaciones vegetales. Se describieron aspectos de su reproducción en términos de cronología reproductiva, tamaño de puesta, duración del período de incubación, permanencia de los polluelos en el nido, morfometría de nidos y huevos, y caracterización del sitio de nidificación en cuanto a la altura de los nidos y especie y altura de las plantas utilizadas como sitio de nidificación. Se localizaron 89 nidos durante las dos temporadas reproductivas, 43 en el año 2006 y 46 en el 2007. El período reproductivo se extendió desde finales de marzo hasta julio, abarcando 129 días en el año 2006 y 122 días durante el año 2007. Las nidadas tuvieron una duración de 36–56 días (construcción 8,6 ± 2,8 días, puesta 8,6 ± 2,7 días, incubación de 14,0 ± 1,2 días y permanencia de los pichones en el nido 14,5 ± 1,0 días). De los 45 nidos examinados el tamaño de puesta modal fue de tres huevos (88,9 %), encontrándose también nidadas de dos (6,7 %) y cuatro huevos (4,4 %). De 38 nidos con huevos para ambas temporadas, 15 nidos produjeron pichones (32 pichones en el 2006 y 20 pichones en el 2007) y solo tres nidos durante el 2006 (37,5 %) lograron producir volantones, los cuales salieron con éxito del nido. La planta más utilizada como sitio de nidificación fue Acacia macracantha (80 % de los nidos detectados), aunque también se hallaron nidos en otras ocho especies de plantas. Las alturas de ubicación del nido fue de 2,7 ± 1,5 m (n = 82; rango 0,3–6,4 m) y la distancia del nido al dosel de la planta utilizada como sustrato fue de 1,1 ± 0,9 m (n = 80; rango 0,1–5,4 m).

Morphometric and cladistic analyses of the phylogeny of Macropodinium (Ciliophora : Litostomatea : Macropodiniidae)

Phylogenetic studies of the genus Macropodinium were conducted using two methods; phenetics and cladistics. The phenetic study of morphometrics suggested that the genus could be divided into 3 groups attributable mostly to cell size and shape. The cladistic study also split the genus into 3 groups related to cell size but groups were further distinguished by patterns of ornamentation. Reconciliation of both approaches revealed considerable congruence, however, it also suggested the existence of convergences in the phenetic study and a lack of resolution in the cladistic study. The morphological diversity of Macropodinium is probably due to evolutionary trends such as increasing body size, allometry and polymerisation of structures. None of these trends, however, was uniformly directional and differential effects were observed in different regions of the phylogenetic tree. Comparison of the phylogeny of Macropodinium to a consensus phylogeny of the macropodids revealed limited incongruence between the 2 trees. The ciliate groups could be related to 2 host groups; the wallaby genera and the kangaroo and wallaroo subgenera. The association with these host groups may be the result of phyletic codescent, ecological resource tracking or a combination of both. Further studies of both host and ciliate phylogeny are necessary to resolve these effects.

The Thelastomatoidea (Nematoda : Oxyurida) of two sympatric Panesthiinae (Insecta : Blattodea) from southeastern Queensland, Australia: taxonomy, species richness and host specificity

The thelastomatoid fauna of two species of wood-burrowing cockroach (Blattodea, Blaberidae), Panesthia cribrata and Panesthia tryoni tryoni, from Lamington National Park, Australia, is described. The following eight new species and three new genera of thelastomatid are proposed: Bilobostoma exerovulva n. g., n. sp.; Cordonicola gibsoni n. sp.; Coronostoma australiae n. sp.; Desmicola ornata n. sp.; Hammerschmidtiella hochi n. sp.; Malaspinanema goateri n. g., n. sp.; Travassosinema jaidenae n. sp.; and Tsuganema cribratum n. g., n. sp. Additional data are given for Blattophila sphaerolaima and Leidynemella fusiformis. Of the 11 species reported, nine were found in P. cribrata and ten in P. tryoni tryoni. Such levels of thelastomatoid species richnessness in single host species are exceptional. Only the mole cricket, Gryllotalpa africana (23), and the domestic cockroach, Periplaneta americana (20), have higher reported richness. Three species, T jaidenae, C. australiae and D. ornata, were found either exclusively or significantly more prevalently in P tryoni tryoni than in R cribrata. Species of Travassosinema, Coronostoma and Desmicola have been found previously only in millipedes (Diplopoda), a fact that suggests that there is a greater degree of niche overlap between R tryoni tryoni and millipedes than for R cribrata.

Basal chromodorid sperm ultrastructure (Nudibranchia, Gastropoda, Mollusca)

The relationship between three genera considered basal in the Chromodorididae (Cadlina, Tyrinna, Cadlinella) has not yet been resolved by traditional morphological means. Here we examined the sperm ultrastructure of Tyrinna nobilis, Tyrinna evelinae, Cadlina flavomaculata and Cadlina cf. nigrobranchiata, with the expectation of finding phylogenetically informative characters. No Tyrinna or Cadlina species showed sperm similarities to Cadlinella. Both Cadlina species and Tyrinna nobilis (but not T. evelinae) exhibited coarse striations in the acrosomal pedestal. The putative fibers that occurred between the coarse striations of the pedestal are condensed into a layer in Cadlina and Tyrinna, but not in other species that also have coarse striations (Gymnodoris), and may constitute evidence for a close relationship. Tyrinna evelinae possessed fine acrosomal striations, which was shared with other Chromodorididae, Actinocyclidae and the cryptobranchs Rostanga and Aphelodoris. We also examined the sperm ultrastructure of 'Chromodoris' ambiguus, an animal which has shown molecular affinities to species of Cadlina, and not Chromodoris. The sperm of 'C'.' ambiguus did not exhibit the typical Cadlina characteristics, but also showed important differences to other investigated Chromodoris species.

New Thelastomatoidea (Nematoda : Oxyurida) from Australian burrowing cockroaches (Blaberidae : Geoscapheinae, Panesthiinae)

Four new species and two new genera of thelastomatoid are described from several species of Australian burrowing cockroaches (Blattodea: Panesthiinae; Geoscapheinae). Corpicracens munozae n. g., n. sp., Pseudodesmicola botti n. g., n. sp. and Cephalobellus nolani n. sp. are described from Geoscapheus dilatatus (Blattodea: Geoscapheinae) from Mendooran, New South Wales; one new thelastomatid, Blattophila praelongicauda n. sp., is described from Panesthia cribrata from Lamington National Park, Queensland. Corpicracens munozae n. g., n. sp. is long and slender, with a monodelphic female reproductive system, a clavate corpus with a slight posterior pseudobulb, oval eggs flattened at the poles, and a relatively robust, subulate tail. Pseudodesmicola botti n. g., n. sp. is slightly more robust in body, also has a monodelphic reproductive system, a cylindrical corpus with a posterior pseudobulb, ovoid eggs and a very long, subulate tail. Cephalobellus nolani n. sp. is distinguished from other members of the genus by its relatively short and broad body and egg shape. Lastly, Blattophila praelongicauda n. sp. is distinguished from other members of the genus by having eggs with a single, polar operculum, tail length, and position of the vulva, nerve ring and excretory pore. An additional species, known by a single specimen from Panesthia tryoni tryoni from the same locality is characterised but not named. The species found are all relatively rare parasites of Australian burrowing cockroaches, each having a prevalence of less than 10%.

Fragilariopsis kerguelensis images from sediment core PS1768-8

Background: Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. In these applications, usually large numbers of frustules need to be identified and / or measured. Although there is a need for automation in these applications, and image processing and analysis methods supporting these tasks have previously been developed, they did not become widespread in diatom analysis. While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into a readily applicable workflow accessible to diatomists exists. Results: The newly developed tool SHERPA offers a versatile image processing workflow focused on the identification and measurement of object outlines, handling all steps from image segmentation over object identification to feature extraction, and providing interactive functions for reviewing and revising results. Special attention was given to ease of use, applicability to a broad range of data and problems, and supporting high throughput analyses with minimal manual intervention. Conclusions: Tested with several diatom datasets from different sources and of various compositions, SHERPA proved its ability to successfully analyze large amounts of diatom micrographs depicting a broad range of species. SHERPA is unique in combining the following features: application of multiple segmentation methods and selection of the one giving the best result for each individual object; identification of shapes of interest based on outline matching against a template library; quality scoring and ranking of resulting outlines supporting quick quality checking; extraction of a wide range of outline shape descriptors widely used in diatom studies and elsewhere; minimizing the need for, but enabling manual quality control and corrections. Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification problems.

The use of close-range photogrammetry in zooarchaeology : Creating accurate 3D models of wolf crania to study dog domestication

Acknowledgements We thank the Muséum National d'Histoire Naturelle, Paris, that provided access to the specimens, and access to the morphometric platform where the surface scans were performed. We also thank Raphael Cornette and Julien Claude for the fruitful discussions we had when writing the manuscript. This work was supported by NERC (grant number NE/K003259/1) and the European Research Council (ERC-2013-StG 337574-UNDEAD). This is publication ISEM 2016-127. We thank the two anonymous reviewers who greatly helped to improve the manuscript.

Ocean acidification and its potential effects on the early life-history of non-calcifying and calcifying echinoderm (Odontaster validus, Patiriella regularis and Arachnoides placenta) larvae, 2011

Ocean acidification, as a result of increased atmospheric CO2, has the potential to adversely affect the larval stages of many marine organisms and hence have profound effects on marine ecosystems. This is the first study of its kind to investigate the effects of ocean acidification on the early life-history stages of three echinoderms species, two asteroids and one irregular echinoid. Potential latitudinal variations on the effects of ocean acidification were also investigated by selecting a polar species (Odontaster validus), a temperate species (Patiriella regularis), and a tropical species (Arachnoides placenta). The effects of reduced seawater pH levels on the fertilization of gametes, larval survival and morphometrics on the aforementioned species were evaluated under experimental conditions. The pH levels considered for this research include ambient seawater (pH 8.1 or pH 8.2), levels predicted for 2100 (pH 7.7 and pH 7.6) and the extreme pH of 7.0, adjusted by bubbling CO2 gas into filtered seawater. Fertilization for Odontaster validus and Patiriella regularis for the predicted scenarios for 2100 was robust, whereas fertilization was significantly reduced in Arachnoides placenta. Larval survival was robust for the three species at pH 7.8, but numbers declined when pH dropped below 7.6. Normal A. placenta larvae developed in pH 7.8, whereas smaller larvae were observed for O. validus and P. regularis under the same pH treatment. Seawater pH levels below 7.6 resulted in smaller and underdeveloped larvae for all three species. The greatest effects were expected for the Antarctic asteroid O. validus but overall the tropical sand dollar A. placenta was the most affected by the reduction in seawater pH. The effects of ocean acidification on the asteroids O. validus and P. regulars, and the sand dollar A. placenta are species-specific. Several parameters, such as taxonomic differences, physiology, genetic makeup and the population's evolutionary history may have contributed to this variability. This study highlights the vulnerability of the early developmental stages and the complexity of ocean acidification. However, future research is needed to understand the effects at individual, community and ecosystem levels.

San Francisco Coastal System grain size and geochemical data for sand provenance study

Over 150 million cubic meter of sand-sized sediment has disappeared from the central region of the San Francisco Bay Coastal System during the last half century. This enormous loss may reflect numerous anthropogenic influences, such as watershed damming, bay-fill development, aggregate mining, and dredging. The reduction in Bay sediment also appears to be linked to a reduction in sediment supply and recent widespread erosion of adjacent beaches, wetlands, and submarine environments. A unique, multi-faceted provenance study was performed to definitively establish the primary sources, sinks, and transport pathways of beach sized-sand in the region, thereby identifying the activities and processes that directly limit supply to the outer coast. This integrative program is based on comprehensive surficial sediment sampling of the San Francisco Bay Coastal System, including the seabed, Bay floor, area beaches, adjacent rock units, and major drainages. Analyses of sample morphometrics and biological composition (e.g., Foraminifera) were then integrated with a suite of tracers including 87Sr/86Sr and 143Nd/144Nd isotopes, rare earth elements, semi-quantitative X-ray diffraction mineralogy, and heavy minerals, and with process-based numerical modeling, in situ current measurements, and bedform asymmetry to robustly determine the provenance of beach-sized sand in the region.