Brooding as response to ocean acidification

Platynereis massiliensis

Anthropogenic atmospheric carbon dioxide (CO2) is being absorbed by seawater resulting in increasingly acidic oceans, a process known as ocean acidification (OA). OA is thought to have largely deleterious effects on marine invertebrates, primarily impacting early life stages and consequently, their recruitment and species’ survival.

Researchers at Plymouth University have found that polychaete worms located around volcanic vents in the Mediterranean grow and develop their eggs within the protection of the family unit - in contrast to closely-related species that release them into the water column to fend for themselves.

The team found that 12 of the 13 species that had colonized the vent area exhibited brooding characteristics, most notably producing fewer and larger eggs that were usually retained within some form of protective sac. Ten of those species were in higher abundance around the vents than in the ambient areas surrounding them -- some by a ratio as high as nine-to-one.

The observation that brooding worms dominated the CO2 vent areas, and existing evidence of physiological and genetic adaptation in vent-inhabiting species, prompted the researchers to take immature adult Platynereis dumerilii specimens and attempt to cross breed them in the laboratory. A male - taken from the ambient control area - and a female - from the vent zone - almost immediately began to breed. But instead of the typical broadcast pattern, the eggs produced were five times larger than the average and were laid in a complex tube structure or brooding pouch.

DNA Barcoding revealed that worms from inside the CO2 vents were from a sibling species, Platynereis massiliensis, one that has diverged from Platynereis dumerilii relatively recently.

One of the most interesting annelid worms here typically grows to around 3cm in length and is found on the seafloor. It was previously thought that their breeding is triggered by a full moon, when they swim up to the surface and release - or 'broadcast' - their eggs. But our studies at the CO2 vents off Ischia have found something very different: those species living near the volcanic vents, in waters rich in carbon dioxide, seem to have adapted to the harsher conditions by brooding their offspring.

The study confirms the idea that some marine organisms have evolved brooding characteristics in response to environmental stresses, such as ocean acidification:

This study brings us one step closer to understanding which marine species will be more resilient to climate changes. In fact, our work helps in establishing a fundamental principle to be used to guide decisions on the conservation of marine ecosystems and to help better manage the fisheries and aquaculture industries.

Fast ploidy assessment in carps

Grass carp (Ctenopharyngodon idella), have been introduced throughout the Midwest and South of the US to clear ponds choked with weeds. However, the release of fertile fish is illegal and so is the purchase or trade in Ohio and surrounding states. For the very same reason they are used as biological control agents grass carp pose a number of threats. They eat soft-stem vegetation - the kinds of plants that dominate coastal marshes which are prime breeding grounds for game fish and act as filters that clear the water.

Hatcheries are breeding carp, but shock their eggs with drastic changes in water pressure. The shock results in a triploid animal and the third set of chromosomes inhibits the production of viable gametes and causes individuals to be reproductively sterile These sterile fish can then be responsibly used for biological control of invasive aquatic plants, but the release of fertile fish could result in growing populations that could devastate the Great Lakes ecosystems. Although the pressure shock method of creating triploid grass carp is nearly 100 % effective, a small proportion of diploid individuals are produced and those have already been found in in Lake Erie's western basin.

Current methods of determining ploidy of an individual require the use of rather expensive laboratory equipment and cannot be performed under field conditions. Researchers have now developed a fast, inexpensive technique to distinguish diploid and triploid grass carp under field conditions using a compound microscope. The shape of the nuclei in red blood cells of carps looks different depending upon whether the fish has a pair or three or more sets of chromosomes. The proportion of abnormally shaped nuclei grows with the increasing number of chromosomes. 

The colleagues smear a drop of fish blood on a slide, let it dry and fix it with methanol. They then stain the slide to bring out the nucleus, and, after rinsing and drying, view it under a standard microscope. Sterile triploid grass carp have a noticeably larger proportion of red blood cells with abnormal nuclei.

The study also included a blinded test to confirm the diagnostic reliability of the visual assessment of ploidy. By viewing blood-smear slides, 14 of 15 staff and interns of the Natural Resources department of Cleveland Metroparks correctly identified the fish; only a single intern incorrectly identified a single fish's reproductive potential.

This test has the potential to be very helpful. The results are pretty convincing, but I would like to see it field-tested by management agencies.

Catastrophic invertebrate extinction

Carelia turricula

The IUCN Red List contains only 733 animal species and 99 plant species listed as extinct since around 1600, a minuscule fraction of total biodiversity, commonly estimated at 5–10 million species. This extinction rate (around 2 species/year) is of the same order of magnitude as the natural background rate based on the fossil record. Such statistics are used by environmental skeptics to downplay the loss of biodiversity.

However, among animals, the focus on birds and mammals and the proportionately negligible assessment of invertebrates masks a real crisis. Although assessment of extinction for all invertebrates is impossible, it may be possible for certain, perhaps representative, groups. Such assessments might permit broad extrapolation and more realistic evaluation of true overall extinction levels.

Mollusks are such a group. Despite the relative lack of focus on invertebrates, almost as many mollusks (311) are listed as extinct by the IUCN (2014) as all chordates combined (338); most (282) are gastropods and half of these (138) Pacific island land snails. Nonetheless, almost twice as many mollusks as are listed as extinct on the IUCN Red List are considered extinct by mollusk specialists, yet the number assessed remains a tiny fraction of the 80,000–100,000 described species and perhaps up to 200,000 real species.

Hawaiʻi has been called the “extinction capital of the world.” But, with the exception of the islands’ birds, there has been no accurate assessment of the true level of this catastrophic loss. Invertebrates constitute the vast majority of the species that make up Hawaiʻi’s formerly spectacularly diverse and unique biota. A team of researchers of the US and France focused on the most diverse group of Hawaiian land snails, the family Amastridae, of which 325 species have been recognized - all known only from Hawaiʻi. They did a rigorous assessment of extinction for this group. 

The colleagues now published their alarming results. Only 15 of these species could still be found alive, and it is estimated that the rate of extinction may have been as high as 14 percent of the fauna per decade. 

In a companion study, members of the team, in collaboration with mathematics and bioinformatics specialists at the Pierre and Marie Curie University in Paris, addressed invertebrate extinction globally. Since the 1980s, many biologists have concluded that the earth is in the midst of a massive biodiversity extinction crisis caused by human activities. Yet only around 800 of the planet’s 1.9 million known species are officially recorded as extinct by the IUCN Red List. Skeptics have therefore asked, “Is there really a crisis?"

We showed, based on extrapolation from a random sample of land snail species from all over the world, and via two independent approaches, that we may already have lost 7 percent (130,000 extinctions) of all the animal species on Earth.

This loss far exceeds official numbers that are primarily based on assessments of birds and mammals and essentially excludes invertebrates, even though invertebrates constitute roughly 99 percent of known biodiversity.

Based on their findings, the researchers show that the biodiversity crisis is real and stressed the need to include assessments of invertebrates in order to obtain a more realistic picture of the current situation, known widely as the sixth mass extinction.

h/t Mario Thomas

Climate change and species distribution

Climate change strongly impacts biodiversity, putting some species at risk of extinction. However, some plant species for example adapt to the new conditions, and go on to thrive and invade areas where they have never grown before.

The black seed grass (Alloteropsis semialata) is the only species known to comprise of individuals that  use both the more common C3 photosynthetic pathway and a pathway called C4, which is a complex combination of leaf anatomical characters and enzymatic reactions that together increase productivity in warm and dry environments. The C4 pathway is present in just three percent of all plant species yet accounts for one quarter of the terrestrial primary production. This impressive productivity is due to C4 grasses, which dominate most open areas of the tropics and subtropics and especially savannahs.

Through genomic analyses a team of international researchers, led by the University of Sheffield were able to understand the ecological changes that happened during the dispersal of Alloteropsis semialata, first in Africa and then in Asia and Australia. The team found that while the non-C4 plants remained confined to a small range of ecological conditions in Central Africa, the evolution of C4 photosynthesis immediately broadened the ecological conditions where the species could grow. C4 plants can disperse broadly across environmental and geographical space, while still surviving in the same habitats occupied by their non-C4 ancestors, showing that this physiological novelty increases the variety of habitats available, which allowed the rapid colonization of three distinct continents.

In a world rapidly affected by climate changes and other anthropogenic alterations of natural systems, understanding how physiological attributes allow some plants to thrive in a variety of conditions might hold the key to the management of more resilient ecosystems. In addition, understanding what allows some plants to be productive in a variety of environments could help direct future crop improvement projects.

Only 12 more days

Only 12 more days to go before we welcome the world to the 6th International Barcode of Life Conference. The level of excitement, anticipation, anxiety and stress here at the institute is increasing by the day. Everyone is working hard to make this a memorable and enjoyable experience for all our guests. 

The Scientific Organizing Committee has put together a densely packed program with invited plenary presentations, contributed sessions, discussion panels, and social events. The conference will start with a full day of pre-conference workshops on August 17, with BOLD and next-generation sequencing workshops held in the morning. Tours to BIO are also offered throughout the day. The afternoon will be devoted to presentations and discussions for forming the International Society for the Barcode of Life. The day ends with a welcoming reception.

Each day of the main conference (August 18-21) will start with plenary presentations in the mornings, ensuring that a component of the conference experience is shared by all delegates. Afternoons will be comprised of parallel sessions, and a dedicated poster session will be held on the afternoon of August 19. Opportunity for dialogue and refreshment will be provided through shared breakfasts, lunches, and coffee breaks each day.

Here a draft schedule of the parallel sessions (please note that some of the sessions can still be moved around): 

The conference program will be augmented by special plenary presentations and a discussion on the State of Biodiversity on the evening of August 19, to be held at the River Run Centre in downtown Guelph. A Gala Reception will be August 20 at the historic and scenic Cambridge Mill.

We will be tweeting, facebooking, and blogging from the conference and during the time leading up to it. We are also looking into options to stream and record sessions of the conference using Periscope. Stay tuned.

Conservation genetics in Latin America

A recently published special issue of the Journal of Heredity focuses on case studies of real-world applications of conservation genetics in Latin America, from nabbing parrot smugglers to exposing fraudulent fish sales. The discipline of conservation genetics has been growing for at least four decades. But only relatively recently have genetic techniques such as DNA Barcoding been used not only to understand conservation issues, but to solve those problems as well. The application of such genetic techniques becomes increasingly important in Latin America, where the vast biodiversity is in decline due to an inexorable economic development. 

Latin America has an unusual level of biodiversity, and is also undergoing unprecedented development, making the region of particular conservation concern. But these factors also contribute to the growth of a scientific community able to provide real help, given the right support.

That support began a decade ago with the establishment of La Red de Genética para la Conservacion (ReGeneC). ReGeneC provides an annual intensive course in conservation genetic techniques and applications for South American students and researchers. ReGeneC's work thus far culminated in a conference in Caracas, Venezuela in May 2014; many of the projects presented at the conference became part of the special issue which includes fifteen papers highlighting the use of genetic techniques to address problems in the conservation of Latin American biodiversity, ranging from trees to toads to tamarins:

• Delimiting Evolutionarily Significant Units of the Fish, Piaractus brachypomus (Characiformes: Serrasalmidae), from the Orinoco and Amazon River Basins with Insight on Routes of Historical Connectivity
  
• Contrasting Genetic Structure and Diversity of Galaxias maculatus (Jenyns, 1848) Along the Chilean Coast: Stock Identification for Fishery Management
  
• Conservation Genetics of the Scalloped Hammerhead Shark in the Pacific Coast of Colombia
  
• Population Structure of mtDNA Variation due to Pleistocene Fluctuations in the South American Maned Wolf (Chrysocyon brachyurus, Illiger, 1815): Management Units for Conservation
  
• Population Structure and Genetic Diversity of the Endangered South American Giant Otter (Pteronura brasiliensis) from the Orinoco Basin in Colombia: Management Implications and Application to Current Conservation Programs
  
• Genetic Variation and Structure in Contrasting Geographic Distributions: Widespread Versus Restricted Black-Tailed Prairie Dogs (Subgenus Cynomys)
  
• Population Genetic Structure in Hyacinth Macaws (Anodorhynchus hyacinthinus) and Identification of the Probable Origin of Confiscated Individuals
  
• Population Genetics of Jaguars (Panthera onca) in the Brazilian Pantanal: Molecular Evidence for Demographic Connectivity on a Regional Scale
  
• Effects of Forest Fragmentation on Genetic Diversity of the Critically Endangered Primate, the Pied Tamarin (Saguinus bicolor): Implications for Conservation
  
• Reduced Genetic Diversity and Increased Dispersal in Guigna (Leopardus guigna) in Chilean Fragmented Landscapes
  
• Identifying Genetic Hotspots by Mapping Molecular Diversity of Widespread Trees: When Commonness Matters
  
• Evolution and Conservation on Top of the World: Phylogeography of the Marbled Water Frog (Telmatobius marmoratus Species Complex; Anura, Telmatobiidae) in Protected Areas of Chile
  
• DNA Barcoding Identifies Illegal Parrot Trade
  
• When You Get What You Haven’t Paid for: Molecular Identification of “Douradinha” Fish Fillets Can Help End the Illegal Use of River Dolphins as Bait in Brazil
  
• Founded: Genetic Reconstruction of Lineage Diversity and Kinship Informs Ex situ Conservation of Cuban Amazon Parrots (Amazona leucocephala)
  

Enjoy reading.

Equine ringworm and minks

Dermatophytosis is a condition caused by an infection of the skin in a variety of mammals such as humans, pets and domesticated animals. It is usually referred to as "ringworm", but this is a misnomer, as the condition is caused by fungal species of the genus Trichophyton and not by parasitic worms. These fungi feed on keratin present in the outer layer of skin, hair, and nails. The probably most well known dermatophytosis is the athlete's foot caused by Trichophyton rubrum or Trichophyton mentagrophytes.

The condition commonly known as equine ringworm starts out with small skin lesions from which the hair is lost. These spread and usually become scurfy. In many cases there may only be a couple of lesions but if left untreated and especially if spread by grooming, the condition can become extensive. The infection is highly contagious and whole groups of horses can become affected in an outbreak. It is possible but uncommon for people to catch Trichophyton equinum from horses:

Reports of dermatophytosis caused by Trichophyton equinum outside of the regular equine host range are rare and limited to dogs and cats, as well as multiple cases of zoonosis of humans who have been in direct contact with infected horses.

The more surprising is its occurrence on some mink from farms in Canada as reported in July. 

This report details 2 outbreaks of dermatophytosis in 2 different mink ranches. On the first farm, only kits were affected, while on the second farm, small numbers of adults were infected. Affected mink were otherwise clinically healthy and in good body condition.

Researchers cultured the dermatophyte and used DNA Barcoding (ITS) to identify the species. It was identified as Trichophyton equinum. Not only are dermatophytosis infections relatively uncommon in farmed mink, infections are usually caused by different fungal species.

In dealing with an outbreak of dermatophytosis, environmental disinfection and separation of infected animals from noninfected animals is paramount in order to control and limit the spread of the pathogen.Systemic antifungal treatment is recommended to shorten the course of the infection and reduce dissemination to other animals.

Knowing the exact species that caused the infection will allow for a more specific treatment that is likely more efficient.

I cannot resist but suggest that society should seriously think about the need for fur farms in general. Fur clothing might be one of the oldest form of clothing but does a modern society still need that especially if the main reason to wear it comes from the wish to show off ones wealth? I don't think so.