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 Like all sources of information, DNA sequences come in various degrees of quality and reliability. To identify, proof, and discard compromised molecular data has thus become a critical component of the scientific endeavor – one that everyone generating sequence data is assumed to carry out before using the sequences for research purposes.

"Many researchers find sequence quality control difficult, though", says Dr. Henrik Nilsson of the University of Gothenburg and the lead author of a new article on sequence reliability, published in the Open Access journal MycoKeys. "There just isn’t any straightforward document to put in their hands to give them a flying start. As a result, scientists differ in the degree to which they are aware of the need to exercise sequence quality control and in what measures they take." Previous studies have highlighted several shortcomings of publicly available DNA sequences – more than ten percent of the fungal DNA sequences may be misidentified at the species level, for example.

"A second complication", adds co-author Prof. Urmas Koljalg of the University of Tartu, "is that the software available for sequence quality management tend to be very complex and resource intensive. It borders on the unfair to expect everyone to have access to, and to master, such computer environments. Fortunately, a whole lot can be done towards quality control of DNA sequences using just manual means and a web browser. The current MycoKeys paper describes these means to help those biologists who do not have a strong background in computer science."

The article – "Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences" – compiles principles and observations to assist the reader in the quality management of sequence data. Although focusing on fungi, the guidelines are general and apply to most groups of organisms and genes. The guidelines target traditional DNA sequencing and are broadly applicable to datasets used in systematics, taxonomy, and ecology.

Co-author Dr. Martin Hartmann of the Swiss Federal Research Institute WSL concludes, "We hope that our guidelines will assist the readers in sharpening their datasets so that, eventually, the trend of increasing noise in the public sequence databases can be arrested. Molecular data offer so much promise that we simply cannot afford to lose accuracy to bias and artifacts."

Original source:
Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, Schoch CL, Nylander JAA, Bergsten J, Porter TM, Jumpponen A, Vaishampayan P, Ovaskainen O, Hallenberg N, Bengtsson-Palme J, Eriksson KM, Larsson K-H, Larsson E, Kõljalg U (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4: 37-62. doi: 10.3897/mycokeys.4.3606

Electronic publishing of new animal species allowed by new rules of the International Code of Zoological  Nomenclature (ICZN)

In a highly debated decision, the rules for publication of scientific zoological names have changed to allow purely digital publications to meet the requirements of the stringent Code of Zoological Nomenclature. On 4th of September, the International Commission on Zoological Nomenclature (ICZN) has passed an amendment that considers a publication in a digital scientific journal ‘legitimate’ if meeting archiving criteria and the publication is registered at the ICZN’s official online registry, ZooBank. The Amendment was published simultaneously in the journals ZooKeys and Zootaxa.

The decision has been contentious because the rules of the ICZN are considered to be among the most rigorous in scientific publication. The task of keeping information straight on animal names is immense and critical, as almost all data on the living world is linked through organismal names. Animals comprise the vast majority of multicellular species recognised (currently around 1.8 million, growing at a rate of about 20,000/year) and for each of these taxa, there are as many as 2-10 legitimately published names due to past debate and poor information exchange. Estimates of the total of living animal biodiversity are 4-20 times this number (8-50 million species).

The change in ICZN publication rules is intended to speed the process of publishing biodiversity information, to improve access to this information, and to help reduce the ‘taxonomic impediment’ that hinders cataloguing of the living world. The move, however, is seen by some as a risky experiment in unmooring a previously well-anchored system of linking publications, names and taxonomic concepts.

The ICZN ruling is explicit that while the publication can exist in an electronic-only format, it still must be published through a journal or book that has an ISSN or ISBN (International Standard Serial Number or International Standard Book Number) and should indicate that it will be archived for long term access. Purely web options such as blog posts, forums, Wikimedia, Wikipedia, Scratchpads and other potentially ephemeral, unarchived web-only sources still do not qualify as legitimate publications under the new ICZN rules.

In practical terms this means:

1) The work must be registered in ZooBank prior to publication
2) The work itself states the date of publication and includes the registration record number (LSID) at ZooBank
3) The ZooBank registration record contains the ISSN or ISBN of the piblication venue (journal or book0  and the name of an electronic archive where the work is intended to be preserved

“The change in ICZN publication rules is intended to speed the process of publishing biodiversity information, to improve access to this information, and to help reduce the ‘taxonomic impediment’ that hinders our cataloguing of the living world. The new rules will open the door to electronic publication and facilitate a truly web-based taxonomy!”, said Dr Ellinor Mitchel, Executive Secretary of ICZN.

Contact
Dr Ellinor Michel, Executive Secretary, ICZN
Tel: +44-207-942-5653 or mobile +44-750-607-1547
Email: iczn-em@nhm.ac.uk

Original source
International Commission on Zoological Nomenclature (2012) Amendment of Articles 8, 9, 10, 21 and 78 of the International Code of Zoological Nomenclature to expand and refine methods of publication. ZooKeys 219: 1–10. doi: 10.3897/zookeys.219.3944
The paper was published simultaneously also in the journal Zootaxa.

Additional Information:
The International Commission on Zoological Nomenclature is an international body of experts on scientific nomenclature who act as the arbiter on scientific names of animals. The Commission’s job is to ensure names of animals are stable and universal by applying the rules of the International Code of Zoological Nomenclature, or occasionally by overriding the rules of the Code to better serve stability. www.iczn.org

The Natural History Museum is a world-leading science research centre and also winner of Visit London’s 2010 Evening Standard’s Peoples Choice Best London for Free Experience Award and Best Family Fun Award. Through its collections and scientific expertise the Museum is helping to conserve the extraordinary richness and diversity of the natural world with groundbreaking projects in more than 70 countries. www.nhm.ac.uk

Ensuring that species names mean what people think they mean is critical for reliable science, and normally the first example of a species that is described is the type specimen. A core role of natural history museums is to house and preserve type specimens, anchoring our information on biodiversity. The Natural History Museum in London has the largest collection of type specimens in the world.
 

5 new species of cuckoo bees from the Cape Verde Islands

The biota of island archipelagos is of considerable interest to biologists. These isolated areas often act as ‘evolutionary laboratories’, spawning biological diversity rapidly and permitting many mechanisms to be observed and studied over relatively short periods of time. Such islands are often the places of new discoveries, including the documentation of new species.

The Republic of Cape Verde comprises 10 inhabited islands about 570 kilometers off the coast of West Africa and have been known since at least 1456. Although the bee fauna of the islands was thought to be moderately well known, research by Dr. Jakub Straka of Charles University in Prague and Dr. Michael S. Engel of the University of Kansas have shown that this is not the case. A recent study published in the Open Access journal ZooKeys documents the cuckoo bee fauna of the islands, revealing that their entire fauna of cuckoo bee species is in fact new to science.

These bees, like the more widely known cuckoo birds, invade the nests of other host bee species. While the host is out collecting pollen for its brood, the cuckoo bee female enters the nest and deposits her eggs on the food resource. The cuckoo bee egg hatches and the immature promptly dispatches the host egg, leaving the pollen and nectar reserves for itself.

The Cape Verde cuckoos are mostly large, black-and-white species, almost zebra-like in their appearance. However, one species, Chiasmognathus batelkai, is quite small, merely 3.2 – 4.2 millimeters in length. Despite its small proportions, C. batelkai is still the largest species of its genus, a group which otherwise comprises even more diminutive species. It appears as though at slightly less than 5 mm, C. batelkai is a remarkable case of island ‘gigantism’, whereby founder effects or genetic drift lead to an increased body size in isolated populations during the initial stages of species origination and differentiation.

The researchers are now attempting to explore the diversity of the cuckoo bees’ hosts and also to understand their evolutionary diversification across the archipelago.

Original source
Straka J, Engel MS (2012) The apid cuckoo bees of the Cape Verde Islands (Hymenoptera, Apidae). ZooKeys 218: 77. doi: 10.3897/zookeys.218.3683

An entire group of millipedes previously unknown in Australia has been discovered by a specialist – on museum shelves. Hundreds of tiny specimens of the widespread tropical family Pyrgodesmidae have been found among bulk samples in two museums, showing that native pyrgodesmids are not only widespread in Australia’s tropical and subtropical forests, but are also abundant and diverse. The study has been published in the open access journal ZooKeys.

"Most pyrgodesmid species are so small they could be easily overlooked," explained millipede specialist Dr Robert Mesibov, of the Queen Victoria Museum and Art Gallery in Launceston, Tasmania. "What’s interesting is how thoroughly overlooked they’ve been. We now know there are dozens of native species of these millipedes in our warm, wet forests, stretching over more than 2000 km on Australia’s east coast."

Six new species and three new genera of the colorful, curiously sculptured millipedes have now been described from Australia, all from the state of Queensland.

"It’s a great example of the value of museum collections," said Dr Mesibov. "Scientists from the Queensland Museum and CSIRO Entomology collected bagfuls of leaf litter in hundreds of places over many years. They extracted bugs in bulk from the fresh litter and took out just the ones they were studying, usually beetles. The remaining bugs are in ‘residues’ stored in the Queensland Museum and the Australian National Insect Collection."

Dr Mesibov said it’s not generally appreciated that zoological specialists find most of their new species in museums. "Sure, biological expeditions to previously unexplored places turn up exciting new species. But there are plenty of surprises waiting when you go rummaging through the residues on museum shelves. In this case, it was a whole family of animals not known from Australia."

Original source:
Mesibov R (2012) The first native Pyrgodesmidae (Diplopoda, Polydesmida) from Australia. ZooKeys 217: 63. doi: 10.3897/zookeys.217.3809

Additional Information:
The millipede research was supported by a grant from the Australian Biological Resources Study.

The year 2010 marked the deadline for the political targets to significantly reduce and halt biodiversity loss. The failure to achieve the 2010 goal stimulated the setting up of new targets for 2020. In addition, preventing the degradation of ecosystems and their services has been incorporated in several global and the EU agendas for 2020. To successful meet these challenging targets requires a critical review of the existing and emerging biodiversity policies to improve their design and implementation, say a team scientists in a paper published in the open access journal Nature Conservation.

These and other questions of increasing the "scale-awareness" of policy makers have been actively discussed at a special SCALES symposium at the 3rd European Congress of Conservation Biology (ECCB) in Glasgow on 28th-31st of August 2012. The lead author Dr Riikka Paloniemi from the Environmental Policy Centre, Finnish Environment Institute (SYKE), in Helsinki, Finland, said: "The policies that regulate biodiversity protection and management operate at many administrative levels, employ a range of instruments at different scales, and involve a variety of governmental and non-governmental actors. These actors often have different insights as to what constitutes a scale-challenge and how to deal with it, inevitably leading to contrasting opinions."

"The question of scale has never been so acute before. Neglecting the spatial and temporal scale at which ecosystems functions when designing conservation measures may lead to long-standing negative consequences, and the failure of the 2010 target is one of the best examples of that" added Dr Klaus Henle from the Helmholtz Centre for Environmental Research – UFZ in Leipzig, Germany and coordinator of SCALES.

The main conclusion of the scientists is that scale-related problems, and their potential solutions, are all about improving our understanding of complexity of the processes. Dealing with a number of different scales and scale-mismatches in biodiversity conservation is challenging; it requires an analytical and political framework that is able to assess the adverse impacts of global change, and to implement the relevant policies at the relevant scale.

Original source:
Paloniemi R, Apostolopoulou E, Primmer E, Grodzinska-Jurcak M, Henle K, Ring I, Kettunen M, Tzanopoulos J, Potts S, van den Hove S, Marty P, McConville A, Simila J (2012) Biodiversity conservation across scales: lessons from a science–policy dialogue. Nature Conservation 2: 7-19. doi: 10.3897/natureconservation.2.3144

Additional information:
SCALES (2009) stands for "Securing the Conservation of biodiversity across Administrative Levels and spatial, temporal, and Ecological Scales" and is a European research project. Financed by the 7th EU framework programme for research and development (FP7), SCALES seeks ways to better integrate the issue of scale into policy and decision-making and biodiversity management in the EU. For more information please see: www.scales-project.net

Biodiversity and environmental monitoring is of crucial importance to diagnose changes in the environment and natural populations in order to provide conservation practice with relevant data and recommendations. The information from monitoring is required, for example, for the design and evaluation of biodiversity policies, conservation management, land use decisions, and environmental protection.

Birds are headline indicators of biodiversity due to their worldwide distribution and popularity. More than 600 bird monitoring programs are in place in Europe, resulting in huge investment of effort. Nearly 28,000 people have been involved in the 144 monitoring programs analyzed in the Nature Conservation paper, spending almost 80,000 person days per year. The evaluation was performed in SCALES, a large-scale integrated project funded by the 7th Framework Program (FP7) of the European Union.

At a dedicated SCALES symposium at the 3rd European Congress of Conservation Biology (ECCB) in Glasgow on 28th-31st of August 2012, the lead author Dr Dirk Schmeller from the CNRS, France and guest researcher at the Helmholtz Centre for Environmental Research – UFZ in Leipzig, Germany, commented: "Although popular among conservationists, bird-monitoring practices have never been characterized quantitatively. We undertook a focused questionnaire-based survey to objectively explore the strengths and weaknesses of the massive bird-monitoring effort in Europe. The results indicate a high potential for further improvements to bird monitoring in sampling design, data analysis and involvement of volunteers from the public".

"Variation in space and time can cause a significant deviation in the monitoring results, which may lead to incorrect conservation policy decisions", added Dr Klaus Henle from UFZ and coordinator of SCALES. "Therefore increasing awareness of the spatial or temporal scale at which monitoring has been performed can be of crucial importance!"

To optimize the monitoring practices, the scientists have proposed a range of recommendations. For most monitoring programs, the best data type to be collected is quantitative (count) data, such as number of individuals, which provide an early warning for conservation and policy. Further, monitoring could optimize resource allocation between independent monitoring sites. Importantly, even low variation between sites or years can induce spurious conclusions; hence repetitive sampling of the same sites within a year should be the rule.

In case of limited manpower, Schmeller and colleagues recommend an increase in the number of monitoring samples, even at the expense of the size of each sample. Further, more collaborations between monitoring programs at different scales need to be established, so that the sampled data may be integrated and re-used.

Finally, monitoring coordinators have to make special efforts to attract volunteers. Coordinators need to keep in mind several important points: 1) the specific characters of the local community; 2) having a recruitment strategy for volunteers interested in monitoring; 3) maintaining good communication with the volunteers; 4) having low hierarchies and treat volunteers with respect, and 5) making links to other voluntary organizations to add value to the work. Schmeller adds: "There is no one clear recipe to recruit and keep volunteers, but what is important is to keep in mind that the volunteers sacrifice their spare time for monitoring activities, which are of interest to all society!"

Original source:
Schmeller D, Henle K, Loyau A, Besnard A, Henry PY (2012) Bird-monitoring in Europe – a first overview of practices, motivations and aims. Nature Conservation 2: 41-57. doi: 10.3897/natureconservation.2.3644

Additional information:
SCALES (2009) stands for "Securing the Conservation of biodiversity across Administrative Levels and spatial, temporal, and Ecological Scales" and is a European research project. Financed by the 7th EU framework programme for research and development (FP7), SCALES seeks ways to better integrate the issue of scale into policy and decision-making and biodiversity management in the EU. For more information please see: www.scales-project.net

he New England Banksia is largely restricted to the eastern edge of the New England Tableland, and is common in places along Waterfall Way. Ms Stimpson’s research has raised this flowering plant, until now classified as a variety of the Hairpin Banksia (B. spinulosa), to the taxonomic level of a distinct species. The study was published in the open access journal PhytoKeys.

"I love the Proteaceae – the family of flowering plants that includes the Banksia and Grevillea genera in Australia and Protea in South Africa," Ms Stimpson said. "Surprisingly, molecular evidence in recent years has shown the family’s closest relatives are the Sacred Lotus and the plane trees. Species of Banksia survive in poor soil and still manage to produce marvellous flowers."

Margaret Stimpson wrote the paper in collaboration with Ian Telford, the Curator of the N.C.W. Beadle Herbarium at the University of New England, Professor Jeremy Bruhl, the Director of the herbarium, and Dr Peter Weston, Senior Principal Research Scientist at the National Herbarium of NSW, an international specialist in Proteaceae systematics.

Margaret’s first project as an undergraduate student of botany at UNE was on the Proteaceae, and she’s been collecting specimens ever since. Now working towards enrolling in a doctoral degree program, she said: "There are still species of Banksia out there that merit description, and I hope to test these in a PhD project."

Margaret established the species rank of the New England Banksia by detailed studies of its leaves, flowers, stem and fruit, and considerations of its ecology and distribution. She explained that it has two growth forms, the more common being a multi-stemmed small shrub with many flowers but few seeds. This form occurs where there has been regular burning, and the seeds need exposure to fire to open. The less common form, found where burning has not occurred, is a single-stemmed tree with many flowers and many seeds that open spontaneously without exposure to fire.

Original source:
Stimpson ML, Weston PH, Telford IRH, Bruhl JJ (2012) First instalment in resolution of the Banksia spinulosa complex (Proteaceae): B. neoanglica, a new species supported by phenetic analysis, ecology and geography. PhytoKeys 14: 57-80. doi: 10.3897/phytokeys.14.3415

Invasive species – plants, animals, and microbes introduced to regions beyond their native range – carry a global price tag of $1.4 trillion dollars. They are responsible for the loss of natural resources and biodiversity, damages to infrastructure, and an uptick in infectious diseases.

Not all non-native species pose a threat. Scientists around the world have spent the last several decades teasing apart the conditions that set the stage for debilitating invaders, like giant hogweed, zebra mussels, or gray squirrels. A number of hypotheses have emerged to help predict how natural areas will respond to introduced plants, animals, and microbes.

An analysis of 371 invasion studies using six dominant invasion hypotheses has revealed their predictive power is weakening. The paper’s authors – Jonathan Jeschke, Lorena Gómez Aparicio, Sylvia Haider, Tina Heger, Christopher Lortie, Petr Pyšek, and David Strayer – found empirical support for all six hypotheses declining, with recent studies showing the lowest levels of support. Hypotheses that were too broad or omitted ecosystem interactions fared among the worst, plants proved easier to predict than animals, and, contrary to popular belief, diverse ecosystems were not inherently resistant against invaders. The study was published in the open-access journal NeoBiota.

The paper’s authors comment: "The observed decline effect means our confidence in making sound policy and management decisions based on the six analyzed hypotheses is lower today than it was in the past. Scientists were overly optimistic about the predictive power of these hypotheses. Given that invasive species are an expensive and ever growing problem, this is a situation that needs to be addressed."

Similar "decline effects" have been noted in other disciplines, among them pharmacological research, psychology, and animal behavior. The effect has been attributed to publication bias, inadequate sample sizes, and a tendency of early tests of hypotheses to pick study organisms or systems where positive results are expected.

Lead author Jonathan Jeschke, of Technische Universität München, concludes: "The decline effect is both worrying and fascinating. It’s a phenomenon that should be investigated across disciplines, as medical and psychological researchers have shown its effects can be strong, and it can distort the predictive power of hypotheses."

The paper’s authors offer four solutions to improve current hypotheses in invasion biology: (1) Existing gaps in empirical tests of hypotheses should be filled. The study revealed crucial gaps in empirical studies, showing that most studies have focused on terrestrial plants but have ignored other organisms and aquatic habitats. (2) Existing hypotheses should be specified for groups of organisms and habitats. (3) Interactions of invasive species with their new ecosystems should be regularly considered. The study shows that hypotheses considering such interactions are better supported by empirical evidence than other hypotheses. (4) Revised hypotheses should be rejected if they do not work. Those hypotheses that still lack empirical support after specification for groups of organisms and habitats (solution 2), consideration of invader-ecosystem interactions (solution 3), or another form of revision should be discarded. Scientists should not waste time and resources to continue working with these hypotheses. Instead, fresh ideas and novel hypotheses are needed to further our understanding of biological invasions – something that is essential to effective management in today’s rapidly changing world.

Original source:
Jeschke JM, Gómez Aparicio L, Haider S, Heger T, Lortie CL, Pyšek P, Strayer DL (2012) Support for major hypotheses in invasion biology is uneven and declining. NeoBiota 14: 1-20. doi: 10.3897/neobiota.14.3435

Additional Information:
Kettunen M, Genovesi P, Gollasch S, Pagad S, Starfinger U, ten Brink P, Shine C (2009) Technical support to EU strategy on invasive alien species (IAS) – Assessment of the impacts of IAS in Europe and the EU. Institute for European Environmental Policy (Brussels, Belgium): 1-44 + Annexes.
Lehrer J (2010) The truth wears off. New Yorker Dec 13: 52-57.
Schooler J (2011) Unpublished results hide the decline effect. Nature 470: 437.

Nowadays, an increasing number of rivers and lakes are being invaded by exotic snails, which come from remote regions, and even other continents. Such species represent a threat to native species, as they compete for food or space with them.

This is the case of the mudsnail Potamopyrgus antipodarum. This small aquatic snail is native to New Zealand, and has spread throughout rivers, lakes or streams in Europe, Australia, America and Asia. The invasion success of this mudsnail may be partly due to the ability of females to reproduce without participation of males (i.e. parthenogenesis). This means that only one female is able to start a new population. Besides, the reproductive potential is huge, up to 230 juveniles per female in a year.

But how can these snails disperse from catchment to catchment? If the species were able to tolerate desiccation, it could be transported attached to birds, fishing tools or terrestrial animals. This possibility has been investigated by the Spanish ecologists Álvaro Alonso and Pilar Castro-Díez from the University of Alcalá, whose research was published in the open-access journal NeoBiota.

They performed a laboratory experiment, exposing the snails to different dehydration periods and counting the number of surviving snails. In this way they demonstrated that the mudsnail can survive up to 48 hours out of water. From this finding, two (low-cost) and relatively easy control mechanisms for avoiding the spread of mudsnails emerge: 1) exposing to air of any fishing tools and/or boats for more than 53 hours and 2) avoiding the access of wild and domestic animals to infected rivers or lakes via physical barriers or scarecrows. Such simple measures can actually help to preserve water bodies free of invaders.

Original source:
Alonso A, Castro-Díez P (2012) Tolerance to air exposure of the New Zealand mudsnail Potamopyrgus antipodarum (Hydrobiidae, Mollusca) as a prerequisite to survival in overland translocations. NeoBiota 14: 67-74. doi: 10.3897/neobiota.14.3140

Rare forget-me-nots discovered in the mountains of New Zealand

Two rare species of forget-me-nots have been added to Flora of New Zealand. These new species were discovered in the mountains of the South Island during an expedition led by Dr. Carlos A. Lehnebach. These new species have been described and illustrated in an article published in the open access journal PhytoKeys.

The expedition was part of a major endeavour by a group of botanists at the Museum of New Zealand Te Papa Tongarewa in partnership with Landcare Research aiming to describe and list all forget-me-nots (Myosotis) found in New Zealand. Dr. Lehnebach, who is a curator at the Museum of New Zealand Te Papa Tongarewa, New Zealand, describes the mountains of the South Island of New Zealand as a hotspot for forget-me-nots diversity as over 30 species are found there.

"The diversity of forms, flower color and leaf shape of New Zealand forget-me-nots is really amazing" said Dr. Lehnebach. "New Zealand forget-me-nots are far different from their blue flower relatives commonly found in people’s gardens, and some native species have yellow, pink, or tube-like brown-bronze flowers. New Zealand is also home for the smallest forget-me-not in the world!" he added.

These two new species are extremely uncommon. One is currently known from a single spot where only six plants were found. The other species is habitat-specific and it is only found at the base of limestone bluffs. "Because of the low number of plants and populations currently known for these forget-me-nots, they have been rated as Nationally Critical", said Dr. Lehnebach. This is not unusual for New Zealand forget-me-nots, and many of them are currently threatened.

Original source:
Lehnebach CA (2012) Two new species of forget-me-nots (Myosotis, Boraginaceae) from New Zealand. PhytoKeys 16: 53. doi: 10.3897/phytokeys.16.3602