Four new avian mitochondrial genomes help get to basic evolutionary questions in the late cretaceous

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.

Taxonomy and palaeoecology of Quaternary faunas from caves in eastern tropical Queensland : a record of broad-scale environmental change

Analysis of fossils from cave deposits at Mount Etna (eastern-central Queensland) has established that a species-rich rainforest palaeoenvironment existed in that area during the middle Pleistocene. This unexpected finding has implications for several fields (e.g., biogeography/phylogeography of rainforest-adapted taxa, and the impact of climate change on rainforest communities), but it was unknown whether the Mount Etna sites represented a small refugial patch of rainforest or was more widespread. In this study numerous bone deposits in caves in north-east Queensland are analysed to reconstruct the environmental history of the area during the late Quaternary. Study sites are in the Chillagoe/Mitchell Palmer and Broken River/Christmas Creek areas. The cave fossil records in these study areas are compared with dated (middle Pleistocene-Holocene) cave sites in the Mount Etna area. Substantial taxonomic work on the Mount Etna faunas (particularly dasyurid marsupials and murine rodents) is also presented as a prerequisite for meaningful comparison with the study sites further north. Middle Pleistocene sites at Mount Etna contain species indicative of a rainforest palaeoenvironment. Small mammal assemblages in the Mount Etna rainforest sites (>500-280 ka) are unexpectedly diverse and composed almost entirely of new species. Included in the rainforest assemblages are lineages with no extant representatives in rainforest (e.g., Leggadina), one genus previously known only from New Guinea (Abeomelomys), and forms that appear to bridge gaps between related but morphologically-divergent extant taxa ('B-rat' and 'Pseudomys C'). Curiously, some taxa (e.g., Melomys spp.) are notable for their absence from the Mount Etna rainforest sites. After 280 ka the rainforest faunas are replaced by species adapted to open, dry habitats. At that time the extinct ‘rainforest’ dasyurids and rodents are replaced by species that are either extant or recently extant. By the late Pleistocene all ‘rainforest’ and several ‘dry’ taxa are locally or completely extinct, and the small mammal fauna resembles that found in the area today. The faunal/environmental changes recorded in the Mount Etna sites were interpreted by previous workers as the result of shifts in climate during the Pleistocene. Many samples from caves in the Chillagoe/Mitchell-Palmer and Broken River/Christmas Creek areas are held in the Queensland Museum’s collection. These, supplemented with additional samples collected in the field as well as samples supplied by other workers, were systematically and palaeoecologically analysed for the first time. Palaeoecological interpretation of the faunal assemblages in the sites suggests that they encompass a similar array of palaeoenvironments as the Mount Etna sites. ‘Rainforest’ sites at the Broken River are here interpreted as being of similar age to those at Mount Etna, suggesting the possibility of extensive rainforest coverage in eastern tropical Queensland during part of the Pleistocene. Likewise, faunas suggesting open, dry palaeoenvironments are found at Chillagoe, the Broken River and Mount Etna, and may be of similar age. The 'dry' faunal assemblage at Mount Etna (Elephant hole Cave) dates to 205-170 ka. Dating of one of the Chillagoe sites (QML1067) produced a maximum age for the deposit of approximately 200 ka, and the site is interpreted as being close to that age, supporting the interpretation of roughly contemporaneous deposition at Mount Etna and Chillagoe. Finally, study sites interpreted as being of late Pleistocene-Holocene age show faunal similarities to sites of that age near Mount Etna. This study has several important implications for the biogeography and phylogeography of murine rodents, and represents a major advance in the study of the Australian murine fossil record. Likewise the survey of the northern study areas is the first systematic analysis of multiple sites in those areas, and is thus a major contribution to knowledge of tropical Australian faunas during the Quaternary. This analysis suggests that climatic changes during the Pleistocene affected a large area of eastern tropical Queensland in similar ways. Further fieldwork and dating is required to properly analyse the geographical extent and timing of faunal change in eastern tropical Queensland.

Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocene–Holocene cave deposit on Kangaroo Island, South Australia

Fossils and sediments preserved in caves are an excellent source of information for investigating impacts of past environmental changes on biodiversity. Until recently studies have relied on morphology-based palaeontological approaches, but recent advances in molecular analytical methods offer excellent potential for extracting a greater array of biological information from these sites. This study presents a thorough assessment of DNA preservation from late Pleistocene–Holocene vertebrate fossils and sediments from Kelly Hill Cave Kangaroo Island, South Australia. Using a combination of extraction techniques and sequencing technologies, ancient DNA was characterised from over 70 bones and 20 sediment samples from 15 stratigraphic layers ranging in age from >20 ka to ∼6.8 ka. A combination of primers targeting marsupial and placental mammals, reptiles and two universal plant primers were used to reveal genetic biodiversity for comparison with the mainland and with the morphological fossil record for Kelly Hill Cave. We demonstrate that Kelly Hill Cave has excellent long-term DNA preservation, back to at least 20 ka. This contrasts with the majority of Australian cave sites thus far explored for ancient DNA preservation, and highlights the great promise Kangaroo Island caves hold for yielding the hitherto-elusive DNA of extinct Australian Pleistocene species.

Quantitative estimation of bioturbation based on digital image analysis

Quantitative determination of modification of primary sediment features, by the activity of organisms (i.e., bioturbation) is essential in geosciences. Some methods proposed since the 1960s are mainly based on visual or subjective determinations. The first semiquantitative evaluations of the Bioturbation Index, Ichnofabric Index, or the amount of bioturbation were attempted, in the best cases using a series of flashcards designed in different situations. Recently, more effective methods involve the use of analytical and computational methods such as X-rays, magnetic resonance imaging or computed tomography; these methods are complex and often expensive. This paper presents a compilation of different methods, using Adobe® Photoshop® software CS6, for digital estimation that are a part of the IDIAP (Ichnological Digital Analysis Images Package), which is an inexpensive alternative to recently proposed methods, easy to use, and especially recommended for core samples. The different methods — “Similar Pixel Selection Method (SPSM)”, “Magic Wand Method (MWM)” and the “Color Range Selection Method (CRSM)” — entail advantages and disadvantages depending on the sediment (e.g., composition, color, texture, porosity, etc.) and ichnological features (size of traces, infilling material, burrow wall, etc.). The IDIAP provides an estimation of the amount of trace fossils produced by a particular ichnotaxon, by a whole ichnocoenosis or even for a complete ichnofabric. We recommend the application of the complete IDIAP to a given case study, followed by selection of the most appropriate method. The IDIAP was applied to core material recovered from the IODP Expedition 339, enabling us, for the first time, to arrive at a quantitative estimation of the discrete trace fossil assemblage in core samples.

Synonymization of key pest species within the Bactrocera dorsalis species complex (Diptera: Tephritidae): Taxonomic changes based on a review of 20 years of integrative morphological, molecular, cytogenetic, behavioural and chemoecological data

Bactrocera papayae Drew & Hancock, Bactrocera philippinensis Drew & Hancock, Bactrocera carambolae Drew & Hancock, and Bactrocera invadens Drew, Tsuruta & White are four horticultural pest tephritid fruit fly species that are highly similar, morphologically and genetically, to the destructive pest, the Oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae). This similarity has rendered the discovery of reliable diagnostic characters problematic, which, in view of the economic importance of these taxa and the international trade implications, has resulted in ongoing difficulties for many areas of plant protection and food security. Consequently, a major international collaborative and integrated multidisciplinary research effort was initiated in 2009 to build upon existing literature with the specific aim of resolving biological species limits among B. papayae, B. philippinensis, B. carambolae, B. invadens and B. dorsalis to overcome constraints to pest management and international trade. Bactrocera philippinensis has recently been synonymized with B. papayae as a result of this initiative and this review corroborates that finding; however, the other names remain in use. While consistent characters have been found to reliably distinguish B. carambolae from B. dorsalis, B. invadens and B. papayae, no such characters have been found to differentiate the latter three putative species. We conclude that B. carambolae is a valid species and that the remaining taxa, B. dorsalis, B. invadens and B. papayae, represent the same species. Thus, we consider B. dorsalis (Hendel) as the senior synonym of B. papayae Drew and Hancock syn.n. and B. invadens Drew, Tsuruta & White syn.n. A redescription of B. dorsalis is provided. Given the agricultural importance of B. dorsalis, this taxonomic decision will have significant global plant biosecurity implications, affecting pest management, quarantine, international trade, postharvest treatment and basic research. Throughout the paper, we emphasize the value of independent and multidisciplinary tools in delimiting species, particularly in complicated cases involving morphologically cryptic taxa.

The fossil calibration database - A new resource for divergence dating

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important, and often least appreciated, step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for non-specialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as one key pipeline for peer-reviewed calibrations to enter the database.

Postglacial Early Permian (late Sakmarian-early Artinskian) shallow-marine carbonate deposition along a 2000 km transect from Timor to west Australia

Late Sakmarian to early Artinskian (Early Permian) carbonate deposition was widespread in the marine intracratonic rift basins that extended into the interior of Eastern Gondwana from Timor in the north to the northern Perth Basin in the south. These basins spanned about 20° of paleolatitude (approximately 35°S to 55°S). This study describes the type section of the Maubisse Limestone in Timor-Leste, and compares this unit with carbonate sections in the Canning Basin (Nura Nura Member of the Poole Sandstone), the Southern Carnarvon Basin (Callytharra Formation) and the northern Perth Basin (Fossil Cliff Member of the Holmwood Shale). The carbonate units have no glacial influence and formed part of a major depositional cycle that, in the southern basins, overlies glacially influenced strata and lies a short distance below mudstone containing marine fossils and scattered dropstones (perhaps indicative of sea ice). In the south marine conditions became more restricted and were replaced by coal measures at the top of the depositional sequence. In the north, the carbonate deposits are possibly bryozoan–crinoidal mounds; whereas in the southern basins they form laterally continuous relatively thin beds, deposited on a very low-gradient seafloor, at the tops of shale–limestone parasequences that thicken upward in parasequence sets. All marine deposition within the sequence took place under very shallow (inner neritic) conditions, and the limestones have similar grain composition. Bryozoan and crinoidal debris dominate the grain assemblages and brachiopod shell fragments, foraminifera and ostracod valves are usually common. Tubiphytes ranged as far south as the Southern Carnarvon Basin, albeit rarely, but is more common to the north. Gastropod and bivalve shell debris, echinoid spines, solitary rugose corals and trilobite carapace elements are rare. The uniformity of the grain assemblage and the lack of tropical elements such as larger fusulinid foraminifera, colonial corals or dasycladacean algae indicate temperate marine conditions with only a small increase in temperature to the north. The depositional cycle containing the studied carbonate deposits represents a warmer phase than the preceding glacially influenced Asselian to early Sakmarian interval and the subsequent cool phase of the “mid” Artinskian that is followed by significant warming during the late Artinskian–early Kungurian. The timing of cooler and warmer intervals in the west Australian basins seems out-of-phase with the eastern Australian succession, but this may be a problem of chronostratigraphic miscorrelation due to endemic faunas and palynofloras.

Effects of methyl eugenol feeding on mating compatibility of Asian population of Bactrocera dorsalis (Diptera: Tephritidae) with African population and with B. carambolae

Males of some species included in the Bactrocera dorsalis complex are strongly attracted to methyl eugenol (ME) (1,2-dimethoxy-4-(2-propenyl) benzene), a natural compound occurring in a variety of plant species. ME feeding of males of the B. dorsalis complex is known to enhance their mating competitiveness. Within B. dorsalis, recent studies show that Asian and African populations of B. dorsalis are sexually compatible, while populations of B. dorsalis and Bactrocera carambolae are relatively incompatible. The objectives of this study were to examine whether ME feeding by males affects mating compatibility between Asian and African populations of B. dorsalis and ME feeding reduces male mating incompatibility between B. dorsalis (Asian population) and B. carambolae. The data confirmed that Asian and African populations of B. dorsalis are sexually compatible for mating and showed that ME feeding only increased the number of matings. Though ME feeding also increased the number of matings of B. dorsalis (Asian population) and B. carambolae males but the sexual incompatibility between both species was not reduced by treatment with ME. These results conform to the efforts resolving the biological species limits among B. dorsalis complex and have implications for fruit fly control programs in fields and horticultural trade.

Trapping to monitor tephritid movement: Results, best practice, and assessment of alternatives

Movement of tephritid flies underpins their survival, reproduction, and ability to establish in new areas and is thus of importance when designing effective management strategies. Much of the knowledge currently available on tephritid movement throughout landscapes comes from the use of direct or indirect methods that rely on the trapping of individuals. Here, we review published experimental designs and methods from mark-release-recapture (MRR) studies, as well as other methods, that have been used to estimate movement of the four major tephritid pest genera (Bactrocera, Ceratitis, Anastrepha, and Rhagoletis). In doing so, we aim to illustrate the theoretical and practical considerations needed to study tephritid movement. MRR studies make use of traps to directly estimate the distance that tephritid species can move within a generation and to evaluate the ecological and physiological factors that influence dispersal patterns. MRR studies, however, require careful planning to ensure that the results obtained are not biased by the methods employed, including marking methods, trap properties, trap spacing, and spatial extent of the trapping array. Despite these obstacles, MRR remains a powerful tool for determining tephritid movement, with data particularly required for understudied species that affect developing countries. To ensure that future MRR studies are successful, we suggest that site selection be carefully considered and sufficient resources be allocated to achieve optimal spacing and placement of traps in line with the stated aims of each study. An alternative to MRR is to make use of indirect methods for determining movement, or more correctly, gene flow, which have become widely available with the development of molecular tools. Key to these methods is the trapping and sequencing of a suitable number of individuals to represent the genetic diversity of the sampled population and investigate population structuring using nuclear genomic markers or non-recombinant mitochondrial DNA markers. Microsatellites are currently the preferred marker for detecting recent population displacement and provide genetic information that may be used in assignment tests for the direct determination of contemporary movement. Neither MRR nor molecular methods, however, are able to monitor fine-scale movements of individual flies. Recent developments in the miniaturization of electronics offer the tantalising possibility to track individual movements of insects using harmonic radar. Computer vision and radio frequency identification tags may also permit the tracking of fine-scale movements by tephritid flies by automated resampling, although these methods come with the same problems as traditional traps used in MRR studies. Although all methods described in this chapter have limitations, a better understanding of tephritid movement far outweighs the drawbacks of the individual methods because of the need for this information to manage tephritid populations.

The complexities of knowing what it is you are trapping

The effectiveness of any trapping system is highly dependent on the ability to accurately identify the specimens collected. For many fruit fly species, accurate identification (= diagnostics) using morphological or molecular techniques is relatively straightforward and poses few technical challenges. However, nearly all genera of pest tephritids also contain groups of species where single, stand-alone tools are not sufficient for accurate identification: such groups include the Bactrocera dorsalis complex, the Anastrepha fraterculus complex and the Ceratitis FAR complex. Misidentification of high-impact species from such groups can have dramatic consequences and negate the benefits of an otherwise effective trapping program. To help prevent such problems, this chapter defines what is meant by a species complex and describes in detail how the correct identification of species within a complex requires the use of an integrative taxonomic approach. Integrative taxonomy uses multiple, independent lines of evidence to delimit species boundaries, and the underpinnings of this approach from both the theoretical speciation literature and the systematics/taxonomy literature are described. The strength of the integrative approach lies in the explicit testing of hypotheses and the use of multiple, independent species delimitation tools. A case is made for a core set of species delimitation tools (pre- and post-zygotic compatibility tests, multi-locus phylogenetic analysis, chemoecological studies, and morphometric and geometric morphometric analyses) to be adopted as standards by tephritologists aiming to resolve economically important species complexes. In discussing the integrative approach, emphasis is placed on the subtle but important differences between integrative and iterative taxonomy. The chapter finishes with a case study that illustrates how iterative taxonomy applied to the B. dorsalis species complex led to incorrect taxonomic conclusions, which has had major implications for quarantine, trade, and horticultural pest management. In contrast, an integrative approach to the problem has resolved species limits in this taxonomically difficult group, meaning that robust diagnostics are now available.

Domestication for Conservation of an Endangered Species: The Case of the Wollemi Pine

A small population of tall slender conifers was discovered in 1994 in a deep rainforest canyon of the Wollemi National Park, New SouthWales, Australia. The living trees closely resembled fossils that were more than 65 million years old, and this ‘living fossil’ was recognised as a third extant genus in the Araucariaceae (Araucaria, Agathis and now Wollemia). The species was named the Wollemi pine (W. nobilis). Extensive searches uncovered very few populations, with the total number of adult trees being less than 100. Ex situ collections were quickly established in Sydney as part of the Wollemi Pine Recovery Plan. The majority of the ex situ population was later transferred to our custom-built facility in Queensland for commercial multiplication. Domestication has relied very heavily on the species’ amenability to vegetative propagation because seed collection from the natural populations is dangerous, expensive, and undesirable for conservation reasons. Early propagation success was poor, with only about 25% of cuttings producing roots. However, small increases in propagation success have a very large impact on a domestication program because plant production can be modelled on an exponential curve where each rooted cutting develops into a mother plant that, in turn, provides more rooted cuttings. An extensive research program elevated rooting percentages to greater than 80% and also provided in vitro methods for plant multiplication. These successes have enabled international release of the Wollemi pine as a new and attractive species for ornamental horticulture.

The Miocene of Western Asia; Fossil mammals at the crossroads of faunal provinces and climate regimes

Being at the crossroads of the Old World continents, Western Asia has a unique position through which the dispersal and migration of mammals and the interaction of faunal bioprovinces occurred. Despite its critical position, the record of Miocene mammals in Western Asia is sporadic and there are large spatial and temporal gaps between the known fossil localities. Although the development of the mammalian faunas in the Miocene of the Old World is well known and there is ample evidence for environmental shifts in this epoch, efforts toward quantification of habitat changes and development of chronofaunas based on faunal compositions were mostly neglected. Advancement of chronological, paleoclimatological, and paleogeographical reconstruction tools and techniques and increased numbers of new discoveries in recent decades have brought the need for updating and modification of our level of understanding. We under took fieldwork and systematic study of mammalian trace and body fossils from the northwestern parts of Iran along with analysis of large mammal data from the NOW database. The data analysis was used to study the provinciality, relative abundance, and distribution history of the closed- and open-adapted taxa and chronofaunas in the Miocene of the Old World and Western Asia. The provinciality analysis was carried out, using locality clustering, and the relative abundance of the closed- and open-adapted taxa was surveyed at the family level. The distribution history of the chronofaunas was studied, using faunal resemblance indices and new mapping techniques, together with humidity analysis based on mean ordinated hypsodonty. Paleoichnological studies revealed the abundance of mammalian footprints in several parts of the basins studied, which are normally not fossiliferous in terms of body fossils. The systematic study and biochronology of the newly discovered mammalian fossils in northwestern Iran indicates their close affinities with middle Turolian faunas. Large cranial remains of hipparionine horses, previously unknown in Iran and Western Asia, are among the material studied. The initiation of a new field project in the famous Maragheh locality also brings new opportunities to address questions regarding the chronology and paleoenvironment of this classical site. Provinciality analysis modified our previous level of understandings, indicating the interaction of four provinces in Western Asia. The development of these provinces was apparently due to the presence of high mountain ranges in the area, which affected the dispersal of mammals and also climatic patterns. Higher temperatures and possibly higher co2 levels in the Middle Miocene Climatic Optimum apparently favored the development of the closed forested environments that supported the dominance of the closed-adapted taxa. The increased seasonality and the progressive cooling and drying of the midlatitudes toward the Late Miocene maintained the dominance of open-adapted faunas. It appears that the late Middle Miocene was the time of transition from a more forested to a less forested world. The distribution history of the closed- and open-adapted chronofaunas shows the presence of cosmopolitan and endemic faunas in Western Asia. The closed-adapted faunas, such as the Arabian chronofauna of the late Early‒early Middle Miocene, demonstrated a rapid buildup and gradual decline. The open-adapted chronofaunas, such as the Late Miocene Maraghean fauna, climaxed gradually by filling the opening environments and moving in response to changes in humidity patterns. They abruptly declined due to demise of their favored environments. The Siwalikan chronofauna of the early Late Miocene remained endemic and restricted through all its history. This study highlights the importance of field investigations and indicates that new surveys in the vast areas of Western Asia, which are poorly sampled in terms of fossil mammal localities, can still be promising. Clustering of the localities supports the consistency of formerly known patterns and augments them. Although the quantitative approach to relative abundance history of the closed- and open-adapted mammals harks back to more than half a century ago, it is a novel technique providing robust results. Tracking the history of the chronofaunas in space and time by means of new computational and illustration methods is also a new practice that can be expanded to new areas and time spans.

Avian diversification patterns across the K-Pg boundary: Influence of calibrations, datasets, and model misspecification

Birds represent the most diverse extant tetrapod clade, with ca. 10,000 extant species, and the timing of the crown avian radiation remains hotly debated. The fossil record supports a primarily Cenozoic radiation of crown birds, whereas molecular divergence dating analyses generally imply that this radiation was well underway during the Cretaceous. Furthermore, substantial differences have been noted between published divergence estimates. These have been variously attributed to clock model, calibration regime, and gene type. One underappreciated phenomenon is that disparity between fossil ages and molecular dates tends to be proportionally greater for shallower nodes in the avian Tree of Life. Here, we explore potential drivers of disparity in avian divergence dates through a set of analyses applying various calibration strategies and coding methods to a mitochondrial genome dataset and an 18-gene nuclear dataset, both sampled across 72 taxa. Our analyses support the occurrence of two deep divergences (i.e., the Palaeognathae/Neognathae split and the Galloanserae/Neoaves split) well within the Cretaceous, followed by a rapid radiation of Neoaves near the K-Pg boundary. However, 95% highest posterior density intervals for most basal divergences in Neoaves cross the boundary, and we emphasize that, barring unreasonably strict prior distributions, distinguishing between a rapid Early Paleocene radiation and a Late Cretaceous radiation may be beyond the resolving power of currently favored divergence dating methods. In contrast to recent observations for placental mammals, constraining all divergences within Neoaves to occur in the Cenozoic does not result in unreasonably high inferred substitution rates. Comparisons of nuclear DNA (nDNA) versus mitochondrial DNA (mtDNA) datasets and NT- versus RY-coded mitochondrial data reveal patterns of disparity that are consistent with substitution model misspecifications that result in tree compression/tree extension artifacts, which may explain some discordance between previous divergence estimates based on different sequence types. Comparisons of fully calibrated and nominally calibrated trees support a correlation between body mass and apparent dating error. Overall, our results are consistent with (but do not require) a Paleogene radiation for most major clades of crown birds.

Non-Syndromic Hearing Impairment in India: High Allelic Heterogeneity among Mutations in TMPRSS3, TMC1, USHIC, CDH23 and TMIE

Mutations in the autosomal genes TMPRSS3, TMC1, USHIC, CDH23 and TMIE are known to cause hereditary hearing loss. To study the contribution of these genes to autosomal recessive, non-syndromic hearing loss (ARNSHL) in India, we examined 374 families with the disorder to identify potential mutations. We found four mutations in TMPRSS3, eight in TMC1, ten in USHIC, eight in CDH23 and three in TMIE. Of the 33 potentially pathogenic variants identified in these genes, 23 were new and the remaining have been previously reported. Collectively, mutations in these five genes contribute to about one-tenth of ARNSHL among the families examined. New mutations detected in this study extend the allelic heterogeneity of the genes and provide several additional variants for structure-function correlation studies. These findings have implications for early DNA-based detection of deafness and genetic counseling of affected families in the Indian subcontinent.

Effects of perturbations on estuarine microcosms

Microcosms containing planktonic communities from Chesapeake Bay responded to enrichment with sewage by developing larger standing crops of phytoplankton and zooplankton. Data suggest that increased productivity would be reflected up the food chain but might increase existing problems with dissolved oxygen and might lead to qualitative changes in the composition of the zooplankton. Either phosphorus or nitrogen was removed more rapidly from solution depending on where and when the experimental water was obtained. Increases in standing crop of algae were associated with loss of nitrogen from solution in two experiments and losses of both nitrogen and phosphorus from solution in one experiment.