Monday, March 2, 2015

We're ready!

We really want to thank everyone who applied for this Spring’s 2015 version of the School Malaise Trap Program! This year, we received an overwhelming amount of applicants to the program (some 230 schools) from across Canada. We are thrilled with this response, and as such we hope to be able to increase the Fall 2015 program’s capacity to meet demand. It is because of the school's continued enthusiasm and support of the program that we have become so successful within just two years.

Here is a map of all the selected schools and reference sites. We're very pleased to have traps pretty much everywhere in Canada:

Now we just need to cross all fingers that the Winter retreats in all of Canada before the collecting period starts but we are pretty optimistic despite all polar vortex cases over the last couple of weeks.

Friday, February 27, 2015

Feather mite barcoding

Feather mites are members of several very diverse groups of mites present in almost all groups of birds. They feed mainly on secretions of the uropygial gland of birds. This gland, probably better known as the preen gland or the oil gland, produces preen oil which is believed to help maintain the integrity of the feather structure, provide waterproofing, and - ironically - is supposed to have an anti-parasitic effect. 

The nature of the biological relationship between feather mites and birds is still poorly understood, and empirical studies show a puzzling scenario: some studies have shown that feather mite abundance correlates positively with bird's body condition, while others have found no significant correlation or even negative correlations. In other words it is unclear if feather mites represent true parasites or commensals. Generally, they are thought of as ectoparasites and in some cases they really cause problems for the affected bird (e.g. feather damage).

One of the reasons for the lack of knowledge on their life history might be the fact that feather mite species identification is a really difficult task. Females and immature stages of many taxa are often indistinguishable, and even for males that usually carry the characteristic species traits, accurate identification requires advanced taxonomic skills and a lot of time and patience. 

Here, we tested DNA Barcoding as a useful molecular tool to identify feather mites from passerine birds. Three hundred and sixty-one specimens of 72 species of feather mites from 68 species of European passerine birds from Russia and Spain were barcoded.

The colleagues determined that a 200-bp minibarcode region showed the same accuracy as the full-length DNA Barcode and in addition that it is flanked by regions sufficiently conserved to make them potentially useful for group-specific primers. 

Species identification accuracy was perfect (100%) but decreased when singletons or species of the Proctophyllodes pinnatus group were included. In fact, barcoding confirmed previous taxonomic issues within the P. pinnatus group. Following an integrative taxonomy approach, we compared our barcode study with previous taxonomic knowledge on feather mites, discovering three new putative cryptic species and validating three previous morphologically different (but still undescribed) new species.

Thursday, February 26, 2015

Tracing Leaf Miners

A major challenge in network ecology is to describe the full-range of species interactions in a community to create highly-resolved food-webs. We developed a molecular approach based on DNA full barcoding and mini-barcoding to describe difficult to observe plant – leaf miner – parasitoid interactions, consisting of animals commonly regarded as agricultural pests and their natural enemies.

Leaf miners are plant feeding insects, mainly consisting of flies, moths, and beetles. Many of them are agricultural pests and are therefore considered economically important organisms. They feed on a wide range of plants, which unfortunately also includes cultivated plants and crops. Females lay their eggs either on the leaf surface or in a hole they punctured into the leaf. The hatched larvae will start feeding on leaf tissue making a tunnel which is called 'mine'. 

The problem is that despite their potential impact on a range of commercially important crops, we know only little about leaf miners and their interactions with other species. They are poorly studied organisms, partly due to their cryptic life-cycle which can create major challenges when attempting to incorporate leaf mining insects into complex ecological networks.

A new study is now presenting a novel way to construct precise plant - leaf miner - parasitoid interactions. Morphological identification is very difficult in all the groups and usually requires rearing of collected larvae. However, laboratory rearing is very difficult because collecting infested leaves and rearing adults from larvae within the mines often results in premature death, or one finds the mines empty as the larvae already hatched or moved on to form a new one. In order to overcome these problems the authors of the new study developed a new molecular approach based on DNA Barcoding of remnant DNA within the mines, and it worked quite nicely:

... we show how a molecular approach can be used to determine difficult and cryptic species interactions, even when an adult insect has left its leaf mine. Our molecular approach found more species and interactions than traditional approaches based on insect rearing methods, altering network structure as well as identifying previously unknown species interactions. Thus networks constructed using these molecular methods are better resolved and more useful for network ecologists.

It is very difficult to effectively control for leaf miners. Infected leaves are usually removed and discarded and pruning is often required in the event of a heavy infestation. Many species of leaf miners overwinter in fallen leaves and soil beneath the host plant. Doing a fall clean up can be beneficial in reducing these overwintering sites. In general leaf miner control relies on the use of a combination of cultural practices, including the collection and disposal of infected leaves, as well as the removal of weeds that can act as alternate hosts. That in turn requires extensive knowledge about the species-species interactions. Far more than we know at this point. This new study might help to speed up this process and gain knowledge that eventually will turn into some useful strategies.

Wednesday, February 25, 2015

The fossil calibration database

Fossils are not only fascinating finds that allow a glimpse into past biodiversity, they also provide the age data needed to unlock the timing of major evolutionary events. Very often fossil data are used to calibrate molecular clocks which can reveal the ages of groups that lack good fossil records. An example is shown in the image on the left. I did this analysis about 10 years ago and some values in the tree are marked with an asterisk. These represent calibration points based on fossil records. I also remember quite well but not fondly that finding these dates required a substantial amount of literature research hindered by the fact that a good number of the publications wasn't easily accessible.

Gladly things have changed. This week a new resource for researchers went live, and it is designed to help answer just those kinds of questions. The Fossil Calibration Database is a free, open-access resource that stores vetted fossil data. More than twenty paleontologists, molecular biologists, and computer programmers from five different countries contributed to the design and implementation of this new database.

The launch of the database was accompanied by five peer-reviewed papers and an editorial on the topic published in Palaeontologia Electronica:

  1. Constraints on the timescale of animal evolutionary history
  2. Fossil calibration of Magnoliidae, an ancient lineage of angiosperms
  3. Phylogenetically vetted and stratigraphically constrained fossil calibrations within Aves
  4. Sixteen vetted fossil calibrations for divergence dating of Charadriiformes (Aves, Neognathae)
  5. Four mammal fossil calibrations: balancing competing palaeontological and molecular considerations

This exciting field of study, known as 'divergence dating,' is important for understanding the origin and evolution of biodiversity, but has been hindered by the improper use of data from the fossil record. The Fossil Calibration Database addresses this issue by providing molecular biologists with paleontologist-approved data for organisms across the Tree of Life. 

The authors also promote best practices for justifying fossil calibrations and citing calibrations properly. These best practices have been published a couple of years ago and I would encourage anyone who plans to do some molecular clock work to read that paper before jumping into any analysis.

Tuesday, February 24, 2015

Discoveries of the week #27

The exploration of Earth's biodiversity is an exciting and ongoing endeavour. Here, we report a new species of seadragon from Western Australia with substantial morphological and genetic differences to the only two other known species. We describe it as Phyllopteryx dewysea n. sp. Although the leafy seadragon (Phycodurus eques) and the common seadragon (Phyllopteryx taeniolatus) occur along Australia's southern coast, generally among relatively shallow macroalgal reefs, the new species was found more offshore in slightly deeper waters. The holotype was trawled east of the remote Recherche Archipelago in 51 m; additional specimens extend the distribution west to Perth in 72 m. Molecular sequence data show clear divergence from the other seadragons (7.4–13.1% uncorrected divergence in mitochondrial DNA) and support a placement as the sister-species to the common seadragon. Radiographs and micro-computed tomography were used on the holotype of the new species and revealed unique features, in addition to its unusual red coloration. The discovery provides a spectacular example of the surprises still hidden in our oceans, even in relatively shallow waters.

While researching the two known species of seadragons as part of an effort to understand and protect the exotic and delicate fish, scientists at Scripps Institution of Oceanography made a startling discovery: A third species of seadragon which was named for Mary ‘Dewy’ Lowe, for her love of the sea and her support of seadragon conservation and research, without which this new species would not have been discovered.
no DNA Barcodes (seven genetic markers but no COI, sigh)

Two new species of the genus Zospeum Bourguignat, 1856 are described from caves in the Sierra de Aitzgorri (Gipuzkoa) and the Sierra Salvada (Burgos) in Northern Spain. The taxa Z. vasconicum sp. n. and Z. zaldivarae sp. n. have recently, without a formal name, been included in a molecular study of worldwide members of the Carychiidae. In the present paper, the shell morphology and variation of these species is described and illustrated.

Two new species in the subterranean genus Zospeum. These blind gastropods barely reach 1 mm in shell size and inhabit caves at depths as deep as 950 m. One species is named after the pre-Roman Era Vascones Tribe which is considered albeit disputed the ancestor of the Basque People. The second species is named after Mª Pilar Zaldívar, a biologist and speleologist from the Niphargus Speleological Team, who discovered the species in the 1980’s.

The first species of the small Afrotropical family Ammodesmidae discovered in central Africa (Democratic Republic of the Congo) belongs to the genus Ammodesmus Cook, 1896, which was hitherto known only from two species in western Africa. A key is given to incorporate A. congoensis sp. n., a species also showing an evident sex dimorphism: ♂ densely hirsute, ♀ with much longer and sparser tergal setae.

This new species belongs to a millipede family with members that had only been known  from western Africa (Guinea, Liberia and Ivory Coast), and eastern Africa (Kenya, Tanzania and Malawi). This huge geographical gap has been a mystery for a while. The species was named after the county of origin.
no DNA Barcodes

Paracreptotrema rosenthali sp. n. was discovered in the intestine of Xiphophorus malinche and Pseudoxiphophorus jonesii, collected from the headwaters of Río Malila, tributary of Río Conzintla, in the Río Pánuco basin, Hidalgo, México, during 2008–2009. The new species differs from the five known species of Paracreptotrema Choudhury, Pérez-Ponce de León, Brooks & Daverdin, 2006 by having vitelline follicles that extend from a level anterior to the pharynx to mid-testes, the seminal vesicle which is more extensively folded, and a wider cirrus sac. The new species resembles P. heterandriae in the length of its ceca, which surpasses the posterior margin of the ovary but do not reach the testes. A key to the species of Paracreptotrema is provided.

A newly discovered helminth parasite that infects swordtail fishes.The species is named in honor of Gil G. Rosenthal, co-founder of the CICHAZ field station in Mexico.
no DNA Barcodes

Pseudancistrus kayabi, Pseudancistrus asurini
Two new species of Pseudancistrus, a genus diagnosed by non-evertible cheek plates and hypertrophied odontodes along the snout margin, are described from two drainages of the Brazilian Shield: P. kayabi from the rio Teles Pires (rio Tapajós basin) and P. asurini from the rio Xingu. The new species are distinguished from congeners (P. barbatus, P. corantijniensis, P. depressus, P. nigrescens, P. reus, and P. zawadzkii) by the coloration pattern. Pseudancistrus kayabi has dark bars on the dorsal and caudal fins which are similar to that of P. reus from the Caroní River, Venezuela. Pseudancistrus asurini is unique among Pseudancistrus in having whitish tips of the dorsal and caudal fins in juveniles to medium-sized adults.

And another week with new members of the Loricarid family, perhaps better known as suckermouth catfish. One species is named after the Kayabi indigenous people that inhabited the region of the rivers Arinos, dos Peixes and Teles Pires, in Mato Grosso State, Brazil and the second name refers to the Asurini indigenous peoples who inhabit the right margin and middle portions of Rio Xingu,  in Pará State, Brazil.
no DNA Barcodes

Thismia hongkongensis
A new species, Thismia hongkongensis S.S.Mar & R.M.K.Saunders, is described from Hong Kong. It is most closely related to Thismia brunonis Griff. from Myanmar, but differs in the number of flowers per inflorescence, the colour of the perianth tube, the length of the filaments, and the shape of the stigma lobes. We also provide inferences on the pollination ecology and seed dispersal of the new species, based on field observations and interpretations of morphology. The flowers are visited by fungus gnats (Myctophilidae or Sciaridae) and scuttle flies (Phoridae), which are likely to enter the perianth tube via the annulus below the filiform tepal appendages, and exit via small apertures between the filaments of the pendent stamens. The flowers are inferred to be protandrous, and flies visiting late-anthetic (pistillate-phase) flowers are possibly trapped within the flower, increasing chances of pollen deposition on the receptive stigma. The seeds are likely to be dispersed by rain splash.

A new species in the genus Thismia which comprise of small herbaceous plants with extremely reduced vegetative structures resulting in a lack of chlorophyll. The plants rely solely on fungal symbionts. The species name reflects the geographical origin of the species in Hong Kong.
no DNA Barcodes

Monday, February 23, 2015

Happy Scallops

Yes, this blog is still alive. I was knocked out by disease for a week but I am back and ready to catch up on all things missed. Let's start the new week on a more positive note with some encouraging news.

Fisheries for king and queen scallops is a growing business worldwide and e.g. in the UK it has become a very important one, generating more than 90 million dollar first sale every year. As a result fisheries for scallops have grown dramatically over the past decade, but there are concerns over the damage to the seabed caused by the dredges and trawls normally used to catch them. 

Both the English and Scottish governments have recently declared networks of marine protected areas (MPAs) around their coasts and are currently deciding on how to manage them. However, there are concerns that the preferred option of both governments is to do little to actually restrict fishing within these MPAs despite good experience documented by countries such as the US. New research also confirms that this would be a wasted opportunity.

The first and only fully protected marine reserve in Scotland is Lamlash Bay marine reserve created 2008 off the Isle of Arran, following a decade-long campaign by the local Community of Arran Seabed Trust (COAST) and it is this backing from the local community that has been crucial to its success. COAST assisted with the research and encouraged the community to keep a watchful eye on activities in the area. In other marine reserves illegal fishing has been a problem, but in this case any suspicious activity has been reported to the authorities and in several cases fishing boats have been encouraged to move on by COAST members.

A new study reports on monitoring surveys conducted inside and outside the marine reserve by researchers in the Environment Department at the University of York from 2010 to 2013. Over the course of this new study, the abundance of commercially important juvenile scallops was consistently higher within the reserve than outside. These scallops were strongly associated with seaweeds and other marine life thriving on the seabed within the protected area. The colleagues found strong evidence that protecting Lamlash Bay from fishing has allowed seaweeds, hydroids and other organisms on the seafloor to recover. These animals act as a magnet for settling juvenile scallops which seek out these habitats for shelter, and to mature to adulthood.  Adult scallops showed benefits too. Their size and reproductive capacity was much higher inside the reserve by the end of the study. The resultant high level of breeding within the reserve is likely to be seeding the surrounding fishing grounds.

The authors conclude that protecting some areas from fishing activity can benefit both conservation and fisheries:

Overall, this study is consistent with the hypothesis that marine reserves can encourage the recovery of seafloor habitats, which, in turn, can benefit populations of commercially exploited species, emphasising the importance of marine reserves in the ecosystem-based management of fisheries.

Scallop fisheries are ideally suited to management using protected areas. This approach can protect sensitive habitats, which also act as nursery grounds for scallops and other species, while boosting the overall productivity of the fisheries. We urge the UK governments to create more highly protected areas which can provide this win-win scenario for the management of our oceans.

Friday, February 13, 2015

National Cockroach Project

In 2009, high school students found novel DNA barcode types in American cockroaches (Periplaneta americana) in New York City. These first preliminary results also indicated that cockroaches in certain city neighborhoods of New York share the same genetic makeup but differ from roaches in their neighboring hoods. This led to a new national project for high school students spearheaded by Mark Stoeckle, Rockefeller University, New York. The goal of the project was to learn more about this feared and despised yet ineradicable urban denizen.

The National Cockroach Project was announced in late 2012 called on high school students and other citizen scientists across the US to sample cockroaches and send them in for barcode sequencing. The main questions of the project were:

Do American cockroaches differ genetically between cities?
Do US genetic types match those in other parts of the world?
Are there genetic types that represent undiscovered look-alike species?

Now a little over 2 years later the project came to a close and the results were just published in Scientific Reports:

Our sampling effort generated 284 cockroach specimens, most from New York City, plus 15 additional U.S. states and six other countries, enabling the first large-scale survey of P. americana barcode variation. Periplaneta americana barcode sequences (n = 247, including 24 GenBank records) formed a monophyletic lineage separate from other Periplaneta species. We found three distinct P. americana haplogroups with relatively small differences within (≤0.6%) and larger differences among groups (2.4%–4.7%). This could be interpreted as indicative of multiple cryptic species. However, nuclear DNA sequences (n = 77 specimens) revealed extensive gene flow among mitochondrial haplogroups, confirming a single species.

According to the authors, the most likely explanation for the detected genetic pattern is multiple human-mediated introductions from allopatric source populations followed by global dispersal among commercial centers. In fact, the different haplogroups must have diverged long before human-aided dispersal, even if the highest mutation rate estimates of insect mtDNA are applied.

This project is a great example for a citizen science project that did important research which has been recognized by being published in a peer review journal. Remarkably one of the study authors is a high school student and another one is a college undergrad.