Tuesday, June 30, 2015


Scutigera coleoptrata
Nearly 13,000 species of arthropods are currently classified in the Myriapoda. Although their name suggests they have countless legs, myriapods range from having over 750 legs (Illacme plenipes) to having fewer than ten legs. Their size ranges from microscopic to 30 cm in length. All of them are terrestrial.

There are four groups of myriapods, how they are related to each other is not yet well understood. Two of them, the symphyla and pauropoda, consist of tiny arthropods living in leaf litter and soil, both superficially resemble centipedes. The chilopoda includes the true centipedes which have only one pair of legs per body segment. They are predators; the first pair of appendages on the trunk are modified into a pair of claws with poison glands, which centipedes use to capture prey (usually other arthropods). The bite of large centipedes can cause humans some pain and discomfort, although there are no authenticated cases of human fatalities from centipede bites.

The diplopoda include the millipedes. Millipede segments are formed in early development by fusion of two adjacent embryonic segments; thus, each adult segment of a millipede bears two pairs of legs. Unlike the predatory chilopoda, most millipedes feed on decaying vegetation, although some are carnivorous.

ZooKeys has just published a conference volume on the  16th International Congress of Myriapodology held last year in Olomouc,Czech Republic. The congress organised by the Centre International de Myriapodologie brought together scientists, students and enthusiastic amateurs with specific interest in millipedes, centipedes, symphylans and pauropods, as well as velvet worms. This conference volume contains lots of very interesting articles and I am happy to report that quite a few use DNA Barcoding in their studies. Here they are including hyperlinks:

Monday, June 29, 2015

Antarctic biodiversity

Most people think of the Antarctic continent as a vast, icy waste, and the sea as uniformly populated by whales, seals and penguins. But that's simply not true. There's much biodiversity on land, especially among the micro-organisms, such as bacteria, and the seafloor is very rich in larger unusual species, such as sea spiders and isopods (the marine equivalents of slaters or wood lice). More than 8000 species are known from the marine environment.

An international team of researchers looked at how recent investigations have revealed the continent and surrounding ocean is rich in species. Studies were highly diversified into a variety of distinct ecological regions that differ greatly from each other. The team explicitly focused on demonstrating the diversity of various areas of the Antarctic continent and Southern Ocean, and noted several unusual ways in which patterns of biodiversity are produced in the region. Geothermal, heated areas, such as volcanoes, have played an important role as refuges from icy, glacial conditions on land. At sea, wind has an especially significant effect on diversity. Windier areas have more seabird species. Increasing wind speeds, associated with the ozone hole, have, quite unusually, improved conditions for wandering albatrosses, reducing their travel time and enabling them to become much heavier as adults.

Antarctica and the Southern Ocean have much more biodiversity, structured in more interesting ways than ever previously thought. Sub-glacial micro-organismal life provides an excellent example of a surprising recent discovery

The team also made a brief assessment of the conservation status of biodiversity in the region. The colleagues found that in some cases conservation measures are excellent, e.g. when it comes to the prevention of invasive alien species. For other issues, work by the Antarctic Treaty Parties is still required. For example, the area covered by special protection on land (the equivalent of national parks), and by marine protected areas at sea, is still too small, when measured by global targets such as those of the Strategic Plan on Biodiversity 2011-2020. The team drew particular attention to the need for comprehensive protection of the Ross Sea.

This is one of the planet's last, relatively intact, large marine ecosystems. It is unusual in this respect, and thus provides a suite of globally significant conservation benefits and scientific insights. Ultimately, the region will require a dedicated plan for biodiversity conservation, similar to those being developed for most other regions of the planet. We think there's plenty of appetite for developing it.

Friday, June 26, 2015

School Malaise Trap Program - Spring 2015

We were scrambling a little in the last weeks but here they are (and all the participating schools have them already) - the results of our School program spring run:

Despite the wintry conditions in some parts of Canada the 68 traps on average collected 453 specimens for the collecting period. Our collections group sorted 61,776 specimens and selected 17,290  to  be barcoded. Our final dataset was made up of 15,199 DNA Barcodes (not all  worked and short barcodes were discarded). Using BOLDs BIN analysis we could  determine that an impressive number of 2,968 species were collected over the three week period of the program, 308 of which were brand new to BOLD. The map below shows all of these collection sites, which include elementary schools, secondary schools, and comparison sites (blue markers).

And what was collected? Here an overview pie chart:

I am particularly fond of scorpionflies and one rare find was this little critter (Boreus brumalis). Adults emerge late in the year, and are active on mild winter days when they are often seen on or near the moss in which they develop. As the common name snow scorpionflies suggests, they are often seen on the snow surface. The program started when large parts of the country still had snow which might explain our luck collecting a member of this group in one of our traps

Thursday, June 25, 2015

Antarctic sponges

Sponges constitute an important component of marine ecosystems in the waters around Antarctica. As filter feeders that rely on food particles suspended in the water passing through complex networks of canals lined with flagellated cells, they provide protected niches for many other organisms.
Some 350 sponge species have been described from the seas around Antarctica, many of which occur nowhere else. This high proportion of endemic species most likely is a reflection o the isolation of the continent, which separated from Gondwana around 140 million years ago. Progressive cooling of the climate, together with the development of the Antarctic Circumpolar Current, set up effective barriers to dispersion, and stimulated ecological specialization.

A team of researchers from Germany and New Zealand has now carried out the first comprehensive molecular genetic survey of sponge diversity in Antarctic waters, using DNA Barcoding. The colleagues found out that Antarctic sponges are a surprisingly diverse group. In fact, the degree of species richness found in the waters around the coldest continent is comparable to that found in tropical sponge communities. Their analyses also supports the idea that Antarctic sponges developed as a largely isolated population, descendants from a small number of ancestral forms that evolved in the waters off Gondwana prior to the break-up of the supercontinent. Some species of Antarctic sponges are known to be widespread on the continental coasts, but very little is known about the genetic relationships between them.

In spite of their considerable ecological significance, Antarctic sponges have never before been investigated with modern molecular methods, which permit rapid and unambiguous species identification and yield insights into the evolution of the group. 

Our results make it possible to create a library of DNA barcodes, which can be used for comparative investigations of the group. We can determine, for instance, whether an ostensibly circumpolar species actually represents a single species or a collection of diverse local forms. Such information is of great significance for the conservation and management of the marine resources in the seas around this unique landmass, which is acutely threatened by global climate change.

Wednesday, June 24, 2015

Discoveries of the week #43

Reproduction in arthropods is an interesting area of research where intrasexual and intersexual mechanisms have evolved structures with several functions. The mating plugs usually produced by males are good examples of these structures where the main function is to obstruct the female genitalia against new sperm depositions. In spiders several types of mating plugs have been documented, the most common ones include solidified secretions, parts of the bulb or in some extraordinary cases the mutilation of the entire palpal bulb. Here, we describe the first case of modified setae, which are located on the cymbial dorsal base, used directly as a mating plug for the Order Araneae in the species Maeota setastrobilaris sp. n. In addition the taxonomic description of M. setastrobilaris sp. n. is provided and based on our findings the geographic distribution of this genus is extended to the Northern hemisphere.

A new jumping spider from Mexico.The species name refers to the anatomy of some brittles used as a mating plug,
no DNA Barcode

Despite the alarming rates of deforestation and forest fragmentation, Madagascar still harbors extraordinary biodiversity. However, in many arthropod groups, such as spiders, this biodiversity remains mostly unexplored and undescribed. The first subsocial Madagascan species of the theridiid spider genus Anelosimus were described in 2005 when six new species were found to coexist in the Périnet forest fragment within Andasibe-Mantadia NP. However, this discovery was based only on a few specimens and the extent of this Madagascan radiation has remained unknown. We here report on a thorough survey of >350 colonies from Périnet, and three pilot surveys into additional Madagascar forests (Ambohitantely, Ranamofana, and Montagne d’Ambre). The morphological, molecular and natural history data from these surveys facilitated a revised taxonomy and phylogenetic hypothesis of Madagascan Anelosimus. This subsocial clade currently comprises six previously known (A. andasibe Agnarsson & Kuntner, 2005, A. may Agnarsson, 2005, A. nazariani Agnarsson & Kuntner, 2005, A. sallee Agnarsson & Kuntner, 2005, A. salut Agnarsson & Kuntner, 2005, A. vondrona Agnarsson & Kuntner, 2005) and 10 new species: A. ata sp. n., A. buffoni sp. n., A. darwini sp. n., A. hookeri sp. n., A. huxleyi sp. n., A. lamarcki sp. n., A. moramora sp. n., A. tita sp. n., A. torfi sp. n., A. wallacei sp. n.. With the exception of A. may and A. vondrona, all other species appear to be single forest endemics. While additional sampling is necessary, these data imply a much higher local richness and endemism in Madagascan forests than in any other comparable area globally. The phylogenetic results establish a sister clade relationship between the subsocial Anelosimus in Madagascar and the American ‘eximius group’, and between the solitary A. decaryi on Madagascar and a solitary American clade. These findings imply duplicate colonizations from America, an otherwise rare biogeographical pattern, calling for more detailed investigation of Anelosimus biogeography.

Madagascar is home to an incredible amount of often endemic biodiversity and spiders are no exception to this. But contrary to a lot of charismatic vertebrate groups comprehensive research into spider diversity is largely lacking. This study looks into one genus of cobweb spiders and 10 new species are described most of which restricted to very small areas implying a much higher hidden diversity.

Material of the paederine genera Domene Fauvel, 1873 and Lathrobium Gravenhorst, 1802 from the Dayao Mountains, southern China, is examined. Eight species are identified, three of them described previously and five undescribed. Four species are described and illustrated for the first time: Domene hei Peng & Li, sp. n., Lathrobium jinxiuense Peng & Li, sp. n., L. kuan Peng & Li, sp. n. and L. leii Peng & Li, sp. n. One probably undescribed species of Lathrobium remains unnamed.

A number of new rove beetles from the Dayao Mountains, China. The first species is named to honor a colleague that helped collecting, the second after the type locality. The third name means 'broad' and refers to a rather wide structure in the morphology. The last species was named after another field trip helper.
no DNA barcode

Scapheremaeus gibbus, Scapheremaeus luxtoni
Scapheremaeus gibbus

Two new species of oribatid mites of the genus Scapheremaeus (Oribatida, Cymbaeremaeidae), S. gibbus sp. n. and S. luxtoni sp. n., are described from New Zealand. Scapheremaeus gibbus sp. n. is morphologically most similar to S. humeratus Balogh & Mahunka, 1967, but differs from the latter by the number of notogastral, genital and adanal setae, morphology of bothridial setae, position of adanal lyrifissures and absence of humeral processes. Scapheremaeus luxtoni sp. n. is morphologically most similar to S. yamashitai Aoki, 1970, but differs from the latter by the morphology of notogastral and rostral setae, morphology of leg solenidia φ2 and development of humeral processes. The species Scapheremaeus zephyrus Colloff, 2010 is recorded for the first time in New Zealand. An identification key to the known New Zealand species of Scapheremaeus is provided.

The species of the mite order Oribatida are of economic importance as hosts of various tapeworm species, but also as important contributors to the breakdown of organic material in the soil, very similar to earthworms. Mites are among the most diverse and successful of all the invertebrate groups. About 40 000 species have been described and there are many colleagues that say this is just the tip of the iceberg. Here are two newcomers from New Zealand. One named after some anatomical structure and the other to honor acarologist Malcolm Luxton.
no DNA barcode

Paracolomerus gonglius, Phyllocoptruta beggerianae, Rhyncaphytoptus fuyuniensis
Paracolomerus gonglius

Three new species of eriophyoid mites from Xinjiang Uygur Autonomous Region, China, are described and illustrated. They are Paracolomerus gonglius sp. n. and Phyllocoptruta beggerianae sp. n. collected on Rosa beggeriana Schrenk ex Fisch. & C. A. Mey. (Rosaceae), and Rhyncaphytoptus fuyuniensis sp. n. collected on Cotoneaster ignavus E. L. Wolf (Rosaceae). All eriophyoid mites described here are vagrants on the undersurface of leaves and any apparent damage was not observed.

And even more new mites. This publication presents three new species from China. They belong to a group that has been recognized as containing important agricultural and forestry pests. The first and third species were named after the type locality, number two after its host plant, Rosa beggeriana.
no DNA barcode

Convolvulus austroafricanus, Convolvulus iranicus, Convolvulus peninsularis, Convolvulus xanthopotamicus
A global revision of Convolvulus L. is presented, Calystegia R.Br. being excluded on pragmatic grounds. One hundred and ninety species are recognised with the greatest diversity in the Irano-Turanian region. All recognised species are described and the majority are illustrated. Distribution details, keys to species identification and taxonomic notes are provided. Four new species, Convolvulus austroafricanus J.R.I.Wood & R.W.Scotland, sp. nov., Convolvulus iranicus J.R.I.Wood & R.W.Scotland, sp. nov., Convolvulus peninsularis J.R.I.Wood & R.W.Scotland, sp. nov. and Convolvulus xanthopotamicus J.R.I.Wood & R.W.Scotland, sp. nov., one new subspecies Convolvulus chinensis subsp. triangularis J.R.I.Wood & R.W.Scotland, subsp. nov., and two new varieties Convolvulus equitans var. lindheimeri J.R.I.Wood & R.W.Scotland, var. nov., Convolvulus glomeratus var. sachalitarum J.R.I.Wood & R.W.Scotland, var. nov. are described. Convolvulus incisodentatus J.R.I.Wood & R.W.Scotland, nom. nov., is provided as a replacement name for the illegitimate Convolvulus incisus Choisy. Several species treated as synonyms of other species in recent publications are reinstated including C. chinensis Ker-Gawl., C. spinifer M.Popov., C. randii Rendle and C. aschersonii Engl. Ten taxa are given new status and recognised at new ranks: Convolvulus namaquensis (Schltr. ex. A.Meeuse) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus hermanniae subsp. erosus (Desr.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus crenatifolius subsp. montevidensis (Spreng.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus fruticulosus subsp. glandulosus (Webb) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus capituliferus subsp. foliaceus (Verdc.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus hystrix subsp. ruspolii (Dammer ex Hallier f.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus hystrix subsp. inermis (Chiov.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus rottlerianus subsp. stocksii (Boiss.) J.R.I.Wood & R.W.Scotland, comb. et stat. nov., Convolvulus calvertii subsp. ruprechtii (Boiss.) J.R.I.Wood & R.W.Scotland, stat. nov., Convolvulus cephalopodus subsp. bushiricus (Bornm.) J.R.I.Wood & R.W.Scotland, stat. nov. The status of various infraspecific taxa is clarified and numerous taxa are lectotypified. This account represents a new initiative in terms of taxonomic monography, being an attempt to bring together the global approach of the traditional monograph with the more pragmatic and identification-focussed approach of most current floras while at the same time being informed by insights from molecular systematics.

Not much left to say for me. A comprehensive monograph on this genus the belongs to the family of plants known as Morning glory.
no DNA barcode

Tuesday, June 23, 2015

A flatworm on the move

Photograph by Makiri Sei
Platydemus manokwari, the New Guinea flatworm, is a highly invasive species, already reported in several regions of the Pacific area, and as well as in France. This is the only land planarian that made it on the list of the '100 worst invasive alien species'.  It feeds on land snails and thus represents a danger to endemic species. Very flat, it is about 50 mm long and 5 mm wide. Although it lives on the ground, it is able to climb trees to follow and consume native snails.

A new study published in PeerJ reports on new occurrences of Platydemus manokwari in several additional countries and territories: Singapore, New Caledonia (including mainland and two of the Loyalty Islands), an additional island in French Polynesia, Wallis and Futuna (from two of the islands, Uvea and Futuna), the Solomon Islands, Puerto Rico and Florida, USA - the latter being the first records on the American continent.

Specimens of the flatworm from various territories were identified by their characteristic appearance, a histological study and DNA Barcoding. 

Sequences of COI comprised two haplotypes, “Australian” (with a minor variation on a single nucleotide in a single specimen among 13) and “World” (France, New Caledonia, Singapore, Tahiti, Florida, Puerto Rico; all identical in 19 specimens). The two haplotypes were found together in the same locality only in the Solomon Islands. The difference of 4.8% between the two variants of P. manokwari found here could be either considered as relatively high intraspecific variation, or as evidence for the presence of two different species. In view of the limited morphological and anatomical differences found between specimens with known haplotypes, and the small size of our sample, we provisionally conclude that a single species, Platydemus manokwari, is involved.

The country of origin of Platydemus manokwari is New Guinea, and Australia and the Solomon Islands are the countries closest to New Guinea from which samples were used. This suggest that two haplotypes exist in the area of origin of the species, but that only one of those (the 'World haplotype') has, through human agency, been widely dispersed. 

The record in Florida is of particular concern because it is in mainland America. Until now, infested territories were mostly islands, and a spread from island to island is usually limited. However, the flatworms now established in Florida will not be subject to these limitations. In addition to their natural spread, flatworms can easily be passively spread through infested plants, plant parts and soil. Therefore, Platydemus manokwari could potentially spread from Florida throughout the U.S., and this should be considered a significant threat to North America.

Monday, June 22, 2015

Tiger conservation

Despite intense conservation efforts, there are fewer than 3,200 tigers (Panthera tigris) in the wild, living in less than seven percent of their historical range. When a population is confined to small islands of wilderness, as are tigers, there is a higher risk of inbreeding and loss of genetic diversity, leaving the species with weaker young. To combat this, the American Museum of Natural History has been working with the global wild-cat conservation organization Panthera to establish genetic corridors that allow tigers to seek new territory for prey and new populations for breeding. Tracking individual cats by using genetic markers lets researchers map movement within and between populations.

Genetic tracking has traditionally relied on extracting DNA from scat collected in the wild. But in humid, tropical landscapes--like those in Sumatra, where a number of tigers live--scat often degrades before researchers can find it. Scent sprays left by tigers on trees and overhanging leaves degrade less quickly, and can be detected between two and eight times as frequently as scat. So, to boost the effectiveness of genetic monitoring of tigers in warm regions, the colleagues questioned whether DNA could be extracted from sprays.

For a proof of concept study researchers collected spray samples from three captive tigers in Ontario (I guess those are Sumatran Tigers from the Toronto Zoo) with cotton swabs that were then stored in tubes of buffer to help preserve the DNA. Tiger spray is a combination of anal gland secretions -said, surprisingly, to have a floral scent like citrus -and urine, which contains DNA in the form of cells from the urethra. The researchers were able to amplify microsatellite loci, providing enough information to fingerprint individual tigers, and portions of the sex chromosome to determine whether they are male or female. They also confirmed the species identity by using a mtDNA marker. However, why they chose cytb instead of COI remains a mystery to me.

The results show that DNA taken from tiger spray is just as good or even better than scat in identifying individual tigers and their gender.

Genetic monitoring of tiger source populations is a conservation priority. The utility of this new method is really impactful because it will let us dramatically build upon the number of tigers that can be surveyed and, consequently, increase our understanding of these elusive animals--hopefully before they are gone. We recently spent weeks looking for tiger scat in the field with very little luck. Although this new spray technique wouldn't replace scat studies entirely, we now know that we can use both methods in conjunction to drastically increase our monitoring abilities.

Friday, June 19, 2015

Elephant poaching hotspots

Today the illegal wildlife trade is the world’s fourth largest form of internationally organized crime and African elephant ivory is a major part of that trade. Roughly 50 000 African elephants are now being killed each year from a population of fewer than 500 000 animals. Poaching is driving these iconic animals toward extinction.

In recent years colleagues have used DNA evidence to trace the origin of illegal ivory and thereby helping police. Knowing the primary areas where elephants are poached could help combat ivory trafficking at its source.

In the past DNA from elephant dung, tissue and hair collected across the African continent was used to map genetic signatures for regional populations. A new study by researchers of the University of Washington and Interpol uses different methods to extract DNA from ivory, allowing them to analyze seized contraband and determine the elephant's original population. 

Africa is a huge continent, and poaching is occurring everywhere. When you look at it that way it seems like a daunting task to tackle this problem. But when you look at large ivory seizures, which represent 70 percent of illegal ivory by weight, you get a different picture.

The group used their method to analyze 28 large ivory seizures, each more than half a ton, made between 1996 and 2014. The samples include 61 percent of all large seizures made worldwide between 2012 and 2014.

The colleagues assigned the geographic origin of ivory seizures by statistically matching genotypes from savanna or forest elephants to a geographic-specific allele frequency map of 16 microsatellite DNA loci. All but one of the 28 seizures were concentrated in only four areas. Most seizures made since 2006 were concentrated in just two areas.

The investigations also show a shift in poaching hotspots beginning in 2006. During the earlier years, 1996-2005, most forest elephant ivory analyzed was assigned to the eastern Democratic Republic of Congo, but none of the forest elephant samples after 2005 came from that area. Two seizures of savanna elephant ivory, in 2002 and 2007, came from Zambia, but the country was not represented in any of the samples after 2007.

Recent efforts to curb trafficking have focused on curbing demand, but those seem painfully slow.

When you're losing a tenth of the population a year, you have to do something more urgent -- nail down where the major killing is happening and stop it at the source. Hopefully our results will force the primary source countries to accept more responsibility for their part in this illegal trade, encourage the international community to work closely with these countries to contain the poaching, and these actions will choke the criminal networks that enable this transnational organized crime to operate.

Wednesday, June 17, 2015

Discoveries of the week #42

Examination of the syntypes of Metriocnemus volitans Goetghebuer, 1940 revealed that these specimens belong to the genus Chaetocladius and are not con-specific with Gymnometriocnemus volitans (Goetghebuer, 1940) sensu Brundin (1956) and Sæther (1983). A literature search showed that Gymnometriocnemus kamimegavirgus Sasa & Hirabayashi, 1993 fits well with the species figured and diagnosed by Brundin (1956) as well as with specimens of this species from Norway. We present arguments for Chaetocladius volitans (Goetghebuer) comb. n. and for the use of G. kamimegavirgus for G. volitans sensu Brundin. In addition, we provide DNA barcode data that indicate the presence of at least seven Gymnometriocnemus species in Norway of which six are collected as male adults. Two of these, Gymnometriocnemus (Gymnometriocnemus) pallidus sp. n. and Gymnometriocnemus (Raphidocladius) autumnalis sp. n. are regarded as new to science and diagnosed based on adult male morphology and DNA barcodes. The species Gymnometriocnemus (Gymnometriocnemus) marionensis Sæther, 1969 is re-established and a key to all Holarctic species is provided.

Non-biting midges of the family Chironomidae are notoriously difficult to identify and experts predict a high level of cryptic diversity within this group. These two new species are described from Norway. One has been named after its pale body colour compared to other Holarctic members of the genus, the other's name refes to the time of the year when the type material was collected.

Malalcahuello ocaresi gen. n. & sp. n., from Chile, is described and compared with Campyloxenus pyrothorax Fairmaire & Germain, 1860.

This is probably one of the shortest abstracts I ever came across, short, sharp and to the point. This newly described click beetle represents a new genus and a new species. The genus name refers to the type locality of the beetle, Malalcahuello, in southern Chile. The species is named in honor of Sergio Ocares Figueroa, an excellent insect collector from Chile.
no DNA Barcode

Eostrobilops humicolus Páll-Gergely & Hunyadi, sp. n. is described from Guangxi Province, China. It is characterized by the combination of a small shell (diameter: 2.3–2.4 mm), strongly ribbed dorsal surface, an infraparietal lamella not reaching the callus, and long basal folds. The new species is found approximately 500 and 800 km from the two nearest species E. infrequens (northern Vietnam), and E. diodontina (Hunan, China), respectively. A checklist of extant Eostrobilops Pilsbry, 1927 and Enteroplax Gude, 1899 species is provided. Enteroplax yaeyamensis Habe & Chinen, 1974, Enteroplax kanjiokuboi Minato & Tada, 1992 and Enteroplax taiwanica Minato & Tada, 1992 are moved to the genus Eostrobilops because of the lack of an elevated parietal callus and a peripheral thread. A map showing all Eostrobilops records is provided.

A new species of  terrestrial pulmonate gastropod. The species name means "soil-dwelling", in reference to the fact that this species was found in soil samples.
no DNA Barcode

Four new Epicephala species that feed on the seeds of Glochidion sphaerogynum (Phyllanthaceae) from Yinggeling Mountain Nature Reserves in Hainan Province of China are described: E. domina sp. n., E. impolliniferens sp. n., E. angustisaccula sp. n. and E. camurella sp. n. The latter two species are also associated with Glochidion wrightii. Photographs of adults and genital structures are provided.

Four new leafminers from China, although these species rather feed on the seeds within the fruits of Glochidion sphaerogynum a plant of the family Phyllanthaceae.
no DNA Barcode

Coccoloba floresii
Coccoloba floresii is here described as a new species from Mexico. Morphological characters of the leaf, inflorescence, and fruit show discontinuities among populations of C. floresii and its relatives, C. barbadensis and C. cozumelensis. In addition, C. floresii is exclusive of the tropical dry forests of Central Depression and Plateau of Chiapas (Mexico) at high elevations. 

A new species of the most species rich genus in the smartweed - buckwheat family. The name of the species honors the Mexican botanist José Salvador Flores Guido.
no DNA Barcode

Bambusicola loculata
A new ascomycete species, Bambusicola loculata, inhabiting decaying bamboo, is introduced based on morpho-molecular studies. Bambusicola loculata is characterized by immersed, dark, stromatic and loculate ascostromata, bitunicate, cylindrical-clavate asci and 1-septate, hyaline, narrowly fusiform ascospores, surrounded by an inconspicuous mucilaginous sheath. Maximum likelihood and Bayesian analyses of combined LSU, SSU, RPB2 and TEF1 gene sequence data as well as morphological characters show that our new taxon belongs to Bambusicola, Bambusicolaceae. The new species is compared with other morphologically and phylogenetically similar species.

A new species of sac fungi. I come across species descriptions of fungi not very often. More than reason enough to show this new one. Although there is no ITS barcode, the study authors have done extensive genetic work (4 different markers) to confirm the species' placement.
no DNA Barcode

Monday, June 15, 2015

The peer review crisis

Peer review in science, in which independent scientists who are experts on the subject assess the paper, is the current strategy for ensuring quality and control in scientific research and, therefore, it is essential for the academic world.  However, the peer review system has been criticized especially in recent years.

The main weaknesses are currently related to three aspects: the voluntary nature of the peer review, since 'peers' only participate in the process if they wish, the disparity of review criteria or guidelines produced by scientific journals, and a lack of tangible recognition of the reviewers for their service to the scientific community. All of the above makes the peer review process slow, highly subjective, and results in reviews of greatly varying quality.

This is a serious problem, not only for the scientific community, but also for the publishers, which in the last few years have openly recognized that it is increasingly difficult to secure participation of scientists as reviewers e.g. in the field of ecology, the non-acceptance rate for requests to review articles is 49%.  I can confirm this although it is not necessarily the lack of recognition but more a lack of time. A review of good quality requires time and I simply don't have much of it at my disposal and as a result the number of reviews I can provide is low. It also seems that the number of requests skyrocketed within the last years. 

A group of researchers from Trent University in Peterborough had a closer look at the history of the peer review process and the current situation for the leading journals in the field of ecology and evolution.

We provide historical context for the cultural lag that governs peer review that has eventually led to the system's current structural weaknesses (voluntary review, unstandardized review criteria, decentralized process). We argue that some current attempts to upgrade or otherwise modify the peer-review system are merely sticking-plaster solutions to these fundamental flaws, and therefore are unlikely to resolve them in the long term.

In addition to their historical research the colleagues conducted a survey in 38 selected journals and all of those confirmed that peer reviews were "not consistent", a cross-cutting issue in practically all scientific fields. The problem is that the definition of an ideal peer review is somewhat complex and, currently, even journals with highly organised systems and well defined guidelines struggle with weak reviews. Some mitigating measures have been suggested such as the privatization of peer reviews and making participation mandatory.

Applying correction factors to the h-index -the highest number of articles that an author has published and been cited at least the same number of times-, paying fees to the reviewers or offering them royalties (such as discounts on subscription fees or acknowledgement notes) are some of the proposals. Moreover, some editors are making efforts to homogenize review criteria between them, such as the British Ecological Society, and some review guidelines exist, although there is no agreed criteria on which is the most relevant.

A disparity of methods used by the journals to instruct their reviewers on peer reviews was evident in all cases. This ranged from the complete absence of guidelines and unclear criteria, to more formal systems with forms and defined criteria.

None of the measures proposed to date has the potential to resolve the problems in the long term, because they are partial and not holistic. In our opinion, a contemporary peer review process, in which the current needs of the scientific community are addressed, should be centralized in a platform -independent of journals, whose interests are above all financial- with clear review criteria and guidelines, adjusted according to the scientific field.

The researchers also propose that this centralization ought to be led by scientists, as this would facilitate the standardization of the process, as well as increasing its transparency and reliability.

I am not sure if the paper covers all issues the current peer review system faces. Although I have no doubt that the weaknesses the colleagues identified are root causes for this peer review crisis I am also not sure if the proposed ideas will help to rescue it. 

What do you think? 

Feel free to share your ideas and thoughts using the comments.

Friday, June 12, 2015

Alien species are changing biogeography

Theba pisana (Credit: César Capinha)
When the first explorers sailed around the world they observed that the further away they traveled, the more different species and ecosystems they encountered. Today we know that there are geographical barriers to dispersal. Lineages that were separated for quite some time followed different evolutionary paths and have diverged. However, humans and their goods travelling over the last few centuries have fostered the dispersal of species to new places. This human-mediated dispersal has been hypothesized to homogenize biodiversity and perhaps breaking down biogeographic barries, but this hypothesis had never been tested globally.

An international team of researchers from Portugal, Austria and Germany tested this homogenization hypothesis by analyzing dissimilarities of species composition of 175 species of alien snails across 56 countries and subregions. For each location they mapped the distribution of snails after human-mediated dispersal. Then they went on to look at where these alien species lived before the human-mediated dispersal. 

The study comes in the wake of recent studies that could not find significant trends in biodiversity loss at the local scale over the last decades. 

We therefore took a different angle. We didn't test whether there has been species richness changes in communities over time. Instead we asked how is the similarity between species communities changing. As expected, before human-mediated dispersal, similar communities were found within each major biogeographic region. But after human-mediated dispersal, the communities of aliens follow a completely new pattern and are organized into only two large biogeographic regions: tropics and temperate areas,

Communities of species in temperate areas are more similar to other communities in temperate areas, independently of the continent they live on, and the same is true for tropical communities. Before, human-mediated dispersal, no species were shared by communities separated by more than 11,000 km, and very few species were shared between communities separated by more than 6.500 km. Now, even locations as far away as 20,000 km can share a large number of species.

In the past, geographical distance was the main factor determining community similarity. Now, climate is the major factor, influenced by distance and the extent of trade between countries, particularly those goods that serve as vectors for the transport of snails, such as roof tiles, live plants, vegetables and fruits. This means that for similar climates, the stronger the trade of these products between two countries, the more similar the species communities in those countries become.

The new study is the first global analysis of how invasions are reorganizing biogeographic patterns that took millions of years to form, and it provides evidence that major biodiversity changes are currently underway. The study also confirms the homogenization hypothesis and adds the influence of climate as an additional parameter. Geographic barriers to dispersal seems to disappear, instead climate limits species colonization in new areas. This suggests that globally, communities with similar climate conditions will become increasingly homogeneous. 

Thursday, June 11, 2015

Barcode Bulletin June 2015

Hot off the press - our new Barcode Bulletin:

Citizen science

Today a post on citizen science. This article is taken from The Conversation and describes the importance o citizen science and how people will become more involved in research in the future. Great article but I spare you the original stock photos and sneak in some of our school project ones. The article was written by Philip James, Professor of ecology at the University of Salford.

Every citizen scientist will soon have the tools of a specialist

Ordinary citizens have become increasingly important to scientific research over the past decade. Today, mobile phone technologies, relatively cheap cameras and almost ubiquitous internet connectivity have opened up new opportunities for conservation organisations to engage with ordinary citizens and encourage citizen science. A citizen scientist is a volunteer who collects and/or processes data as part of a scientific enquiry. This could mean noting the plants found on a day trip or more systematically recording wildlife in a special area. While citizen science projects can be in any branch of science, my focus is on wildlife research. The list of citizen science projects is long. This year's BBC Springwatch, which concludes this week, has highlighted a number of mass participation projects in which people can become involved, such as recording the first signs of spring. All such schemes are predicated on the idea that people will go out and report what they see.

But technological advances are also changing the way that professional scientists collect and record data on animals. These changes often require specialised equipment and resources beyond the scope of most amateurs. Now that new technologies are changing the working practices of professional ecologists, what does this mean for citizen science?

DNA testing

Until recently, the way to ascertain the presence of great crested newts in a pond was to go and look. Because the newt is a protected species, disturbing it is illegal. But just looking for the adults or their eggs is not. Today, however, finding great crested newts and other aquatic animals can be done using environmental DNA (eDNA). DNA is released into the water by plants and animals in a host of ways: from their skin, faeces, mucous, hair, eggs and sperm, or when they die. By simply collecting and analysing a water sample from the pond or stream, we can find traces of eDNA and identify the animals living there, even if they are hard to recognise.

DNA barcoding allows species to be identified using short genetic markers in an organism's DNA. And actually, these barcodes can be obtained from tiny amounts of tissue even by non-specialists. All that is required is the correct DNA processing and sequencing technology.

Genetic identification is not the only way in which technological advancement is changing the way that we record the species around us. Noting the birds in a woodland is more often than not a case of listening and identifying the songs rather than seeing the birds themselves. Eco-acoustics or soundscape ecology studies the relationships between animals and their environment based on sound. There are now technologies available that allow birds and amphibian communities to be identified from sound recordings. This means that it will soon be possible to place an audio recorder in the field and walk away while it records birdsong and other sounds over an extended period of time. The aim is that the recordings can be analysed automatically using software to draw up a species list for that area.

Raising standards

But if the collection of wildlife data is to reveal useful information, it needs to be done systematically. Recording the presence of a wildlife species only tells you that it was there at the time that it was recorded. To spot trends, the recording needs to be repeated in the same way over a number of years. This can be difficult when relying on volunteers, but it is not impossible and there are many good examples of systematic surveys, but these are mainly carried out by people with a little more than basic knowledge.

In fact, technology is now progressing to the point that it can do the work of a specialist on behalf of any citizen, helping to standardise measurements and carry out complex analysis instead of just simple observations. For example, a new app enables visitors to the New Forest to search for cicadas - last sighted in the forest in 2000 - by analysing sound recordings of background noise captured with a mobile phone. It's not hard to imagine similar projects asking people to collect and study samples of eDNA or make regular recordings of the dawn chorus using easily available tools. Mass recording of wildlife sightings such as those requested by the BBC and the Mammal Society are not simply about recording wildlife for scientific enquiry. They are about individuals, couples and families going outside, exploring and connecting with their environment. Discovering what is there and being part of a larger group of people. It is about making new discoveries together. But with new technologies, the details of citizen science will change. Future technological advances will present new ways to continue our long established heritage of amateur natural history.

Wednesday, June 10, 2015

Discoveries of the week #41

New records of water mites (Acari: Hydrachnidia) from streams in South Korea are presented. Two species are described as new to science: Torrenticola neodentifera sp. n. (Torrenticolidae) and Atractides ermilovi sp. n. (Hygrobatidae). Five species are reported as first records for Korea: Wandesia (Wandesia) reducta Tuzovskij, 1987, W. (Wandesia) cf. rara Tuzovskij, 1990, Sperchon (Sperchon) orientalis Tuzovskij, 1990, Feltria (Feltria) kuluensis Tuzovskij, 1988 and Atractides (Atractides) constrictus (Sokolow, 1934). The latter species is redescribed and elevated to species rank based on new material from the Russian Far East.

Water mites (Hydrachnidia) are a group of mites covering more than 40 families and 5 000 species found in freshwater and marine habitats.The first new species was named for its similarity with another species of the genus (T. dentifera), and the second after after Sergey Ermilov for his contribution to the taxonomy of oribatid mites
no DNA barcode

Formosiepyris vietnamensis sp. n. (Hymenoptera: Bethylidae) is described based on material collected from Da Lat, southern Vietnam. This is the first record of Formosiepyris Terayama from Vietnam. The new species can be distinguished from other Formosiepyris species by a narrow and rounded clypeus; a mandible with three teeth; a second metasomal tergite having small, sparsely distributed punctures and smooth interspaces, except for anterior 2/5, which is microreticulate; and a head length : width aspect ratio of 10 : 11. A key to the Oriental species of Formosiepyris is provided.

A new species for a family of aculeate wasps with a biology that ranges from parasitism to hunting. The species name refers to the type locality Vietnam.
no DNA barcode

A grapevine leafminer found recently in table grape orchards and vineyards in the Paarl region (Western Cape, South Africa) is described as Holocacista capensis sp. n. It has also been found on native Rhoicissus digitata and bred on that species in the laboratory. It is closely related to Holocacista salutans (Meyrick, 1921), comb. n. (from Antispila), described from Durban in KwaZulu-Natal, but widespread in southern Africa and a native leafminer of various Vitaceae: Rhoicissus tomentosa, R. digitata, R. tridentata and Cissus cornifolia. Holocacista capensis has been found on Vitis vinifera both in Gauteng and Western Cape, the earliest record being from 1950 in Pretoria. The initial host shift from native Vitaceae to Vitis must have occurred much earlier. The species is sometimes present in high densities, but hitherto no sizeable damage to the crops has been noted. The genus Holocacista Walsingham & Durrant, 1909, previously known from the single European grapevine leafminer H. rivillei (Stainton, 1855), is expanded and redescribed and for the first time reported from Africa, East and South-East Asia and Australia. It comprises seven named species and at least 15 unnamed species. The following species are also recombined with Holocacista: transferred from Antispilina: South-African H. varii (Mey, 2011), comb. n., feeding on Pelargonium, transferred from Antispila: the Indian species H. micrarcha (Meyrick, 1926), comb. n. and H. pariodelta (Meyrick, 1929), comb. n., both feeding on Lannea coromandelica, and H. selastis (Meyrick, 1926), comb. n. on Psychotria dalzelii. We also remove the following from Antispila: Heliozela anna (Fletcher, 1920), comb. n. and H. argyrozona (Meyrick, 1918), comb. n., whereas the following Indian Vitaceae feeding species are confirmed to belong in Antispila s. str.: Antispila argostoma Meyrick, 1916 and A. aristarcha Meyrick, 1916. Holocacista salutans and H. varii are redescribed and diagnosed against H. capensis and other South African Heliozelidae. DNA barcodes are provided for 13 species of Holocacista.

Although not specifically stated the species name obviously refers to the type locality at the Western Cape in South Africa. 

Four new species of Cerambycidae are described from Paraguay: Eranina tomentilla (Hemilophini); Mimasyngenes concolor (Desmiphorini); Recchia drechseli (Aerenicini); and Microibidion bimaculatum (Neoibidionini). The new species are included in known keys.

Four new longhorn beetle species from Paraguay. The first name refers to the hairy look of the species, the second to the uniform coloration, the third is named  for Ulf Drechsel, collector of the holotype, and number four after two spots on the wings.
no DNA barcode

In this study we revise the taxonomy of the genus Prionopelta for the Malagasy region, treating seven species, six of which are newly described (P. laurae sp. n., P. seychelles sp. n., P. subtilis sp. n., P. talos sp. n., P. vampira sp. n., P. xerosilva sp. n.), and one redescribed (P. descarpentriesi Santschi). One species, P. seychelles, is restricted to Seychelles, while the six remaining species treated are endemic to Madagascar.

A small ant genus that used to comprise of 15 species, now there are 21. Siz new species from Magagascar.
no DNA barcode

Brevianthus is a distinctive genus of leafy liverwort in its succubously inserted, entire leaves, lack of underleaves, restriction of sexual organs to lateral-intercalary branches, scattered rhizoids and dense leaf-surface ornamentation. The sole species, Brevianthus flavus, is divided into two subspecies, one in Tasmania the other in New Zealand. A second species, Brevianthus hypocanthidium, is described as new and is the first record of the genus for New Caledonia. Among its distinguishing characters are its shallowly bilobed leaves, and triangular underleaves present on small to medium-sized shoot sectors, the lack of a hyaline leaf margin, and the crenulate leaf margin formed by heavily thickened external cell walls. The most unusual features of the new species are the presence of underleaves between lateral leaf insertion lines that reach the ventral stem mid-line, and the absence of underleaves from larger shoots. To explain these features we propose a competitive model of shoot formation wherein the ventral merophyte progressively loses vigor as its relative stature decreases, and its derivative cells become discontinuous and isolated along the ventral stem surface, with intervening areas occupied by derivatives of the more vigorous lateral merophytes.

A new species of liverwort belonging to the monogeneric liverwort family Brevianthaceae which was represented by a single species, Brevianthus flavus. This species was previously thought to be endemic to western Tasmania but was recently collected in New Zealand. 
no DNA barcode

Monday, June 8, 2015

How is it possible that so many large herbivores can coexist in Africa?

Theory holds that these large mammals partition food resources to coexist, which results in a distinct diet. Traditional theories categorize these animals along a spectrum from grass-eating grazers to non–grass-eating browsers. However, little is known about the specific plants that elephants, impalas, zebras and other large herbivores eat. Having a classification with just two categories based on broad plant types seems insufficient.

Researchers from Princeton University, the Smithsonian Institution and the Mpala Research Centre in Kenya used metabarcoding to analyze the feces of seven herbivore species, matching the sequences they found to a reference library of plant DNA which was a combination of EMBL data and the researchers own sequencing efforts.

By sequencing plant DNA from large mammal herbivore fecal samples, we analyzed the diets of an large mammal herbivore assemblage in Kenya. Diet composition was similar within species and strongly divergent across species, irrespective of feeding guild: Grazers ate similar total amounts of grass but different suites of grass species.  Diet composition differed between all species—even pairs of grazers matched in size, digestive physiology, and location—and dietary similarity was sometimes greater across grazing and browsing guilds than within them.

This clear diet partitioning suggests that the coarse trophic categorizations used so far may rather generate misleading conclusions about competition and coexistence of large mammal herbivores. Their diversity might be much more tightly linked to plant diversity. The study results suggest that species-specific plant traits may actually be key to understanding dietary differences.

Our approach could be applicable to environmental management. Wildlife and livestock overlap in rangelands worldwide, and resource competition between them (both real and perceived) is a major source of human–wildlife conflict. However, the extent of dietary overlap is poorly resolved due to the difficulty of studying wildlife diets. Controlled studies using DNA metabarcoding could elucidate the mechanisms of facilitative and competitive interactions as well as identify important forage species, thereby informing management strategies.

Friday, June 5, 2015

Knowing trees, I understand the meaning of patience (Hal Borland)

Despite decades of biological inventories worldwide, we still do not know how many species exist and how they are distributed. Although global patterns of estimated vascular plant species richness and distribution have become more clear, no previous study has focused on trees as a distinct growth form. As a consequence, our estimation of the number of tree species in tropical forests still depends on untested expert opinions rather than on an appropriate methodological framework and data set.

Although we can say with much confidently  'the tropics are diverse,' the answer to 'how diverse' still remains open to speculation. Tropical tree identification is notoriously difficult - hampered by hard-to-access terrain and the sheer number of rare species.

A new study published in PNAS tries to give an answer to the question 'how diverse' by estimating the number of tropical tree species worldwide. This work is a collaborative effort of over 170 scientists from 126 institutions. They analysed a dataset composed of 207 forested locations across tropical America, Africa and the Indo-Pacific. Much of the data came from CTFS-ForestGEO study sites, where standardized pan-tropical survey methods create opportunities to much more accurately gauge tropical diversity. Each forest plot contains at least 250 individual trees identified to species, ensuring comprehensive coverage of the total species diversity in each geographical area.

The global analysis raised the minimum estimated number tree species to at least 40,000 to 53,000 in the tropics, in contrast to only 124 across temperate Europe. Among their findings, the researchers note that, contrary to previous assumptions, the Indo-Pacific tropics contain as much species diversity as tropical America - at least 19,000 species. Both tropical America and the Indo-Pacific are about five times as species-rich as Africa (4,500–6,000 tree species), whose forests are hypothesized to have experienced extensive extinction events during the Pleistocene era of glaciation and climate change. All three regions contain distinct tree lineages reflecting unique evolutionary histories.

The colleagues note that their calculations excluded some 10 percent of unidentifiable trees in the dataset which comprised 657,630 individuals. As these trees could reasonably represent rare or previously unknown species, there's a high likelihood that the world's estimates of total tree species diversity will keep increasing as more of the tropics are surveyed and studied.

By raising the estimated minimum number of tree species in the world, estimates for the number of arthropod and microbe species associated with tropical trees also increases, placing an even higher premium on the protection of these forest ecosystems. 

Meanwhile, as deforestation and development increase the extinction risk for many unique species, lessons may be learned from Africa's reduced tropical diversity. When forest areas shrink, rare species are usually the first to disappear. Consequently, even if the extinction pressure is eventually lifted, a much more limited palette of species remains to repopulate the region. While the tropics are vast and diverse, their individual components are irreplaceable.

The stunningly high tree diversity of the tropics is represented by thousands of rare species, whose sparse populations may not be sustained in the long term by isolated protected areas. This study once again validates a strategy of making forest reserves as big as possible, and also trying to prevent their isolation from adjoining areas of forest.