Phylogeny of Hypselodoris (Nudibranchia: Chromodorididae) with a review of the monophyletic clade of Indo-Pacific species, including descriptions of twelve new species

This work provides an account of the systematics and phylogeny of Hypselodoris . Aspects of the morphology of 42 species are described and the systematic status of an additional 11 species is discussed. Twelve new species are described: Hypselodoris alboterminata, H. bertschi, H. bollandi, H. fucata, H. iacula, H. insulana, H. krakatoa, H. paulinae, H. reidi, H. rudmani, H. violabranchia and H. zephyra. A phylogenetic analysis supports the monophyly of Hypselodoris and Risbecia . Two distinct clades of Hypselodoris are present. One contains species from the Atlantic and eastern Pacific while the other contains species limited to the Indo-Pacific tropics and adjacent temperate regions. Species from the Atlantic and eastern Pacific are bluish in body colour and have a plesiomorphically large receptaculum seminis while Indo-Pacific taxa are variably coloured and all have a minute receptaculum seminis. The distribution and size of mantle glands provides a wealth of morphological characters. With few exceptions, mantle glands vary in closely related species and are important for distinguishing members of smaller clades. Mantle gland distribution is therefore useful in identifying preserved material that is difficult to identify to species in the absence of the pigment of living specimens. Similar colour patterns found in sympatric species of Hypselodoris appear to be a result of both common descent and convergence between less closely related lineages. Biogeographic distributions of sister taxa provide several examples of vicariance. Examination of these cases shows that no single vicariant pattern is present, but vicariance appears to occur at the margins of the Indo-Pacific rather than centrally. Some vicariance occurs even within archipelagos such as the Hawaiian Islands. These cases largely refute the generality of the hypothesis of Springer (1982), that Pacific Plate and Australasian Plate endemic sister taxa should predominate.     

Old mice, young islands and competing biogeographical hypotheses

Naturally occurring variation within a small rodent species native to the southeastern USA, Peromyscus polionotus, has interested biologists for nearly a century. This species has contributed significantly to our understanding of geographical variation and has often been presented as an example of adaptive evolution. Much of the interest in this organism has been predicated on assumptions that the species is relatively young (<300 000 bp) and that coastal populations have a very recent history (<10 000 bp). To test these assumptions and the prevailing biogeographical hypothesis (Recurrent Invasion), we examined nucleotide sequence data from the cytochrome b and D-loop mitochondrial regions (2449 bp) for 79 samples of P. polionotus collected across the Gulf Coast region of Florida and Alabama. Samples representing Peromyscus maniculatus bairdii, P. m. sonoriensis, P. m. pallescens, and P. keeni were used as outgroups. The degree of cytochrome b divergence (approximately 4.4%) between P. maniculatus and P. polionotus was higher than expected. Analyses consistently indicated that three distinct groups are represented within P. polionotus from the Gulf Coast region. Among these, coastal populations (beach mice) form a monophyletic group and apparently represent a substantially older group (approximately 200 000 year. separation) than previously recognized. Our results were counter to the core assumptions of the existing biogeographical model but were consistent with an alternative hypothesis (Shore-line Tracking) which provides a more parsimonious explanation for the observed patterns. This research provides new insight into the evolutionary history of P. polionotus and highlights the importance of considering biogeographical history when evaluating extant patterns of natural variation.     

What's old and new in molecular phylogenetics

While it is fairly easy to devise a phylogenetic tree based on molecular data, it has proven difficult to tell how reliable any such tree is. Thus while the genetic inference that humans, chimpanzees, and gorillas cluster together is widely accepted, the genetic inference that the primary division among Old World human populations is between Asia and EurAfrica is not. A molecular phylogenetic inference linking humans and chimpanzees was proposed in the 1980s based on the technique of DNA hybridization. Despite several recent publications in primary and secondary source material, much confusion still exists surrounding the work. This paper tries to clarify issues that may still be confusing to physical anthropologists, and proposes criteria upon which to judge the robusticity of a phylogenetic inference based on DNA hybridization, in light of a recent published claim of replication. The claim of replication is considered critically. Interestingly, the original DNA hybridization data may actually show a chimp-gorilla link, in harmony with other phylogenetic results.     

Phylogeography of a mite,Halozetes fulvus,reflects the landscape history of a young volcanic island in the sub‐Antarctic

Previous studies of the microarthropods of Marion Island, Southern Ocean, documented high mitochondrial COI (cytochrome c oxidase subunit I) haplotype diversity and significant genetic structure, which were ascribed to landscape subdivision. In this paper we revisit these ideas in light of new geomorphological evidence indicating a major lineament orientated along N26.5°E. Using the microarthropod Halozetes fulvus, we test the hypothesis that the eastern and western sides of the island show different population genetic patterns, corresponding to the previously unrecognized geological separation of these regions, and perhaps also with differences in climates across the island and further landscape complexity. Mitochondrial COI data were collected for 291 H. fulvus individuals from 30 localities across the island. Notwithstanding our sampling effort, haplotype diversity was under‐sampled as indicated by rarefaction analyses. Overall, significant genetic structure was found across the island as indicated by Φ_ST analyses. Nested clade phylogeographical analyses suggested that restricted gene flow (with isolation‐by‐distance) played a role in shaping current genetic patterns, as confirmed by Mantel tests. At the local scale, coalescent modelling revealed two different genetic patterns. The first, characterizing populations on the south‐western corner of the island, was that of low effective population size and high gene flow. The converse was found on the eastern side of Marion Island. Taken together, substantial differences in spatial genetic structure characterize H. fulvus populations across Marion Island, in keeping with the hypothesis that the complex history of the island, including the N26.5°E geological lineament, has influenced population genetic structure. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 131–145.     

The old wasp and the tree: fossils, phylogeny and biogeography in the Orussidae (Insecta, Hymenoptera)

The phylogenetic relationships of the fossil orussid taxa Mesorussus taimyrensis and Minyorussus luzzi are examined by analysing them together with a large data set compiled previously for the extant Orussidae. The fossils are placed in an unresolved trichotomy with the extant Orussidae. The phylogeny is used for evaluating the hypothesis that the ancestors of the family had reduced body size; the results of this analysis are inconclusive. The biogeographical history of the Orussidae is explored. The common ancestor of the family was probably widespread, the initial splitting events taking place prior to or coinciding with the separation of Laurasia from Gondwana. Later putative vicariance events can be correlated with the gradual breakup of Gondwana. However, the biogeographical history of the Orussidae is dominated by speciation within regions and dispersal. The minimum age of the common ancestor of the Orussidae is >180 Myr when estimated from the biogeographical pattern, >95 Myr when estimated from the phylogenetic position of the fossils; the earlier date is considered to be the most likely.  © 2004 The Linnean Society of London , Biological Journal of the Linnean Society , 2004, 82 , 139–160.     

糖组学研究策略及前沿技术研究进展

糖组学是继基因组学和蛋白质组学后的新兴研究领域,主要研究聚糖结构与功能.通过与蛋白质组数据库结合,糖捕捉法能系统鉴定糖蛋白和糖基化位点.糖微阵列技术可以对生物个体产生的全部蛋白聚糖结构进行鉴定与表征,提高了聚糖分析通量.而化学选择糖印迹技术简化了聚糖纯化步骤并提高了糖基化分析的灵敏度.双消化并串联柱法通过双酶消化双柱分离,在分析聚糖结构的同时也鉴定蛋白质的序列,并与蛋白质组学研究兼容.     

European plant science: a field of opportunities

Plants have a pivotal role in eco- and agricultural systems.Genomics is driving a rapid expansion of our understanding ofhow genes, individually and in networks, determine plant function.Technological developments in breeding and genomics are providingstrategies to translate this knowledge into crop improvement.The possibilities range from improvement of existing crops andthe systematic use of natural diversity through to the domesticationof completely new species. As examples of possible goals, itis discussed how profiling of composition will integrate plantbreeding and agronomic practice with emerging knowledge aboutnutrition and health, how improved and novel crops will contributeto the creation of new bio-based economies revolving aroundplant products, and how advances in our knowledge about plant–environmentand plant–pathogen interactions will provide novel strategiesto stabilize agricultural yield in a fluctuating environmentand contribute to integrated approaches in which modern agricultureis carried out in concert with the environment. In addition,knowledge generated by plant science will be needed to monitor,understand, and cope with climate change and its impact on agricultureand ecosystems. Realization of these goals will require closeinteractions with related disciplines including agronomy andecology. Further, it will be important to continue and deepenopen support for research in the developing world. Key words: Agronomic practice, biodiversity, domestication, ecosystems, environment, genomics, novel crops, plant breeding, plant products, yield     

Panbiogeography and conservation science in New Zealand

Abstract

New Zealand’s official conservation science framework, the Protected Natural Areas Programme (PNA), is evaluated in relation to current biogeographic/systematic methods and principles with reference to philosophy, taxonomy, information content, and historical geological/biological relations. The PNA Programme and its parent International Union for Conservation of Nature and Natural Resources (IUCN) framework is based on a phenetic system of classification that does not reflect process (phylogenetic) characters of ecological systems. The PNA philosophy of conservation science is shown to be essentialist, rooted in traditional medieval Western metaphysics, and out of step with current developments in biogeography, systematics, and ecology. Panbiogeography is an appropriate global perspective for developing a conservation science because it meets the requirements of homology, monophyly, increased information content, and empirical testability whereas the PNA programme does not. Establishment of a Panbiogeographic Track Atlas is proposed as a suitable conservation framework for historical ecology and biogeography. The atlas could provide an empirical natural resource inventory to identify priority areas for conservation at an economically acceptable cost compared to the PNA Programme. Application of cladistic techniques to ecological and biogeographic patterns in relation to the Atlas can provide aphylogenetically sound hierarchical classification for conservation science. The potential benefits of the panbiogeographic approach for conservation education and tourism are discussed.     

Molecular genetics of biotin metabolism: old vitamin, new science

Biotin is a water-soluble vitamin that participates as a cofactor in gluconeogenesis, fatty acid synthesis and branched chain amino acid catabolism. It functions as the carboxyl carrier for biotin-dependent carboxylases. Its covalent attachment to carboxylases is catalyzed by holocarboxylase synthetase. Our interest in biotin has been through the genetic disease, "biotin-responsive multiple carboxylase deficiency," caused by deficient activity of holocarboxylase synthetase. As part of these studies, we made the unexpected findings that the enzyme also targets to the nucleus and that it catalyzes the attachment of biotin to histones. We found that patients with holocarboxylase synthetase deficiency have a much reduced level of biotinylated histones, yet the importance of this process is unknown. The dual nature of biotin, as the carboxyl-carrier cofactor of carboxylases and as a ligand of unknown function attached to histones, is an enigma that suggests a much more involved role for biotin than anticipated. It may change our outlook on the optimal nutritional intake of biotin and its importance in biological processes such as development, cellular homeostasis and regulation.     

Marine radiations at small geographic scales: speciation in neotropical reef gobies (Elacatinus)

Studies of speciation in the marine environment have historically compared broad-scale distributions and estimated larval dispersal potential to infer the geographic barriers responsible for allopatric speciation. However, many marine clades show high species diversity in geographically restricted areas where barriers are not obvious and estimated dispersal potential should bring many sister taxa into contact. Genetic differentiation at small (separation < 1000 km) spatial scales could facilitate speciation by mechanisms other than the gradual accumulation of reproductive isolation during extended allopatry, such as ecological adaptation to local environmental conditions or the rapid evolution of genes tied to mate recognition, but the role of each of these possibilities has not been simultaneously explored for any species-rich marine taxon. Here, we develop a robust phylogenetic framework for 31 taxa from a species-rich group of Neotropical reef fishes (Gobiidae: Elacatinus) using 3230 bp from one mitochondrial and two nuclear gene regions. We use this framework to explore the contribution of large- and small-scale geographic isolation, ecological differentiation, and coloration toward the formation and maintenance of species. Although species of Elacatinus occur on both sides of the Isthmus of Panama, no sister species are separated by this barrier. Instead, our results indicate that sister taxa occur within oceans. Sister taxa usually differ by coloration, and more distantly related sympatric species frequently differ by resource use. This suggests that some combination of coloration and ecological differences may facilitate assortative mating at range boundaries or in sympatry. Overall, speciation in Elacatinus is consistent with a model of recurring adaptive radiations in stages taking place at small geographic scales.     

Closing the gap: Avian lineage splits at a young,narrow seaway imply a protracted history of mixed population response

The evolutionary significance of spatial habitat gaps has been well recognized since Alfred Russel Wallace compared the faunas of Bali and Lombok. Gaps between islands influence population structuring of some species, and flightless birds are expected to show strong partitioning even where habitat gaps are narrow. We examined the population structure of the most numerous living flightless land bird in New Zealand, Weka (Gallirallus australis). We surveyed Weka and their feather lice in native and introduced populations using genetic data gathered from DNA sequences of mitochondrial genes and nuclear β‐fibrinogen and five microsatellite loci. We found low genetic diversity among extant Weka population samples. Two genetic clusters were evident in the mtDNA from Weka and their lice, but partitioning at nuclear loci was less abrupt. Many formerly recognized subspecies/species were not supported; instead, we infer one subspecies for each of the two main New Zealand islands. Although currently range restricted, North Island Weka have higher mtDNA diversity than the more wide‐ranging southern Weka. Mismatch and neutrality statistics indicate North Island Weka experienced rapid and recent population reduction, while South Island Weka display the signature of recent expansion. Similar haplotype data from a widespread flying relative of Weka and other New Zealand birds revealed instances of North Island—South Island partitioning associated with a narrow habitat gap (Cook Strait). However, contrasting patterns indicate priority effects and other ecological factors have a strong influence on spatial exchange at this scale.     

Molecular systematics of the Asiatic Viverridae (Carnivora) inferred from mitochondrial cytochrome b sequence analysis

Cytochrome b sequences of 15 species of Viverridae were used to investigate the systematic relationships of the Asiatic Viverridae and their affinities to African viverrid species. Phylogenetic analyses (maximum parsimony and neighbour-joining) supported the hypothesis of paraphyly of the subfamily Viverrinae, whereas the data suggests the monophyly of the two Viverridae subfamilies endemic to Asia. The Asiatic viverrids do not appear to have a unique origin. Results indicate that the Asiatic linsang is less closely related to the other Asiatic taxa, whereas the African civet ( Civettictis ) groups with the Asiatic civets ( Viverra , Viverricula ). The relationships between the three clades — civets, Paradoxurinae, Hemigalinae — cannot be firmly established, but they appear to be closely related together.     

Versatile stem cells, young and old. A review

Both embryonic and somatic stem cells have been studied in recent years with particular regard to their differentiation potential. In vitro studies allow a considerable amplification of such cells in culture as well as the induction of commitment in different directions under proper stimulating factors. Moreover, a surprising versatility has been discovered,which makes possible a `reprogramming' of stem cells into a lineage pathway which may be completely different from the expected direction: for instance, a production of brain cells from blood progenitors has been obtained. It is thus possible to envisage methods of producing in culture sufficient amounts of stem cells, committed to a certain pathway, which can be transplanted in vivo to replace damaged tissues and organs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Small,odd and old: The mysterious Tarsius pumilus is the most basal Sulawesi tarsier

In this study, we present the first genetic evidence of the phylogenetic position of Tarsius pumilus, the mountain tarsier of Sulawesi, Indonesia. This mysterious primate is the only Eastern tarsier species that occurs exclusively in cloud forests above 1800 m.a.s.l. It exhibits striking morphological peculiarities—most prominently its extremely reduced body size, which led to the common name of ‘pygmy tarsier’. However, our results indicate that T. pumilus is not an aberrant form of a lowland tarsier, but in fact, the most basal of all Sulawesi tarsiers. Applying a Bayesian multi-locus coalescent approach, we dated the divergence between the T. pumilus lineage and the ancestor of all other extant Sulawesi tarsiers to 9.88 Mya. This is as deep as the split between the two other tarsier genera Carlito (Philippine tarsiers) and Cephalopachus (Western tarsiers), and predates further tarsier diversification on Sulawesi by around 7 Myr. The date coincides with the deepening of the marine environment between eastern and western Sulawesi, which likely led to allopatric speciation between T. pumilus or its predecessor in the west and the ancestor of all other Sulawesi tarsiers in the east. As the split preceded the emergence of permanent mountains in western Sulawesi, it is unlikely that the shift to montane habitat has driven the formation of the T. pumilus lineage.     

First record of Amphisbaena anomala (Squamata: Amphisbaenidae) in lowland Caatinga based on citizen science,with an updated distribution map

Amphisbaena anomala is a species of worm lizard endemic to Brazil, with most known records in eastern Amazonia, but also occurring in northern Cerrado and at highland moist forest enclaves in Caatinga. Based on citizen science data, we report a new easternmost and southernmost locality for A. anomala, representing its first record in the lowlands of the Caatinga ecoregion. The new record, in Abaiara, Ceará, Brazil is 335 km southeast from the nearest previously documented occurrence of the species. We conducted a comprehensive literature review, updating the species known distribution map with three times more records than the last update, and describing the soil types and ecoregions where the species is typically found. The new record reinforces the crucial role of taxonomists in the identification of species in citizen science platforms, assisting in narrowing existing gaps in biogeographic knowledge. Furthermore, we draw attention to the lack of specimen collection in some environmental impact assessments, from which some photos on citizen science platforms come.