Legless lizards

Legless lizards, represented by more than 200 species worldwide, are well-adapted to life in loose soil. Fascinatingly, lizards on five continents independently lost their limbs in order to burrow more quickly into sand or soil, making them a great textbook example for convergent evolution. Some still have vestigial legs. Though up to 20 cm in length, these reptiles are rarely seen because they live mostly underground, eating insects and larvae, and may spend their lives within an area of one square meter. 

In an earlier genetic study of the California legless lizard (Anniella pulchra) researchers revealed five deep genetic lineages:

These genetic lineages of Anniella are diagnosable with two independently evolving markers (mt and nuDNA), showing that these lineages are, or were historically, independently evolving. Some of the newly discovered lineages are restricted to a few marginal sites in one of the most heavily impacted and degraded regions of California, the San Joaquin Valley. The recognition of several restricted-range lineages of a rare and declining taxon, within a region characterized by intense historical and ongoing habitat destruction, has important conservation implications.

Now, four years later the same researchers describe four new species. Three of the genetic lineages discovered in 2009 can be readily diagnosed through a combination of coloration, scalation, and skeletal characters (trunk vertebra number). A fourth lineage is cryptic, but can be distinguished from the other species by its karyotype, which of course is a bit tedious and makes DNA barcoding more attractive. By the way in the original study a part of COI was also used to determine the lineages. 

The colleagues named the new species after four legendary UC Berkeley scientists: the founder of the  Museum of Vertebrate Zoology at UC Berkeley,  Joseph Grinnell, the paleontologist Charles Camp, philanthropist and amateur scientist Annie Alexander and herpetologist Robert C. Stebbins, at 98 the only one of those still alive.

The former Anniella pulchra, a species of special concern, is now divided into five species. This means A. pulchra has a smaller distribution than previously recognized, thereby enhancing concern about its conservation status. The remaining four species have even smaller ranges, some of which are degraded or threatened by human activities. Whereas much of the range of Anniella stebbinsi is already compromised by urban development, the conservation implications for the other three new species are even more striking because of their very limited distributions. Anniella grinnelli is known from a few sites in the southern San Joaquin Valley, an area that has been greatly modified by urban and agricultural development. Anniella grinnelli persists in small patches within the Bakersfield city limits, but some of the populations we collected were extirpated by development during the course of this study. The type locality at the Sand Ridge Preserve is a secure site that will help ensure the species survival. Anniella alexanderae is known from two sites at the base of the Temblor Mountains, and should be considered rare pending further study. Finally, Anniella campi is known from just three sites. This species may be restricted to the vicinity of potentially fragile springs in canyons that open into the Mojave Desert and so warrants careful monitoring.

A handful of feathers and bird poop

The white-winged flufftail (Sarothrura ayresi) is a bird so rare that bird experts believe there are only 250 of them left in the world. In South Africa, the bird has been spotted in only about 15 sites in the 136 years since it was first described in Potchefstroom. The only other country where this small water bird with big feet has been sighted with any regularity is Ethiopia. So little is known about the bird that the question remains whether the two populations, separated by 4 000km, are linked through migration.

The ornithologist Craig Symes from Wits University would like to find out more about the rare bird. He will be using feather samples from Addis Ababa, in Ethiopia and some South African white-winged flufftail samples. By using isotope analysis he intends to work out if the birds have travelled between the two countries. If the isotope signatures of the samples from the different countries prove similar, it could suggest the birds move between South Africa and Ethiopia.

To understand more about the species, Symes also collected white-wing flufftail faeces in Ethiopia. Through DNA Barcoding he hopes to find out what the birds eat. With that information, conservationists believe the bird can be saved as only with a better understanding of its movements and habits effective conservation measures can be implemented.

A few weeks ago, there was a missed opportunity to add to Symes’s feather collection, when a worker at an airport in Durban found a white-winged flufftail near one of the runways. Unfortunately, by the time the bird was identified, it had been released. It was the first time in more than 100 years that a white-winged flufftail had been spotted in Durban. White-winged flufftail numbers are so low that  representatives from BirdLife say this individual could be one of the last of its species in South Africa.

Seminar

Unfortunately, that is often so true (as are most of Jorge Cham's comics):

Life in Toronto

This weekend you will find a lot of us in Toronto as we join the Ontario BioBlitz.

Just in case you don't know - A BioBlitz is a special type of field study, where a group of volunteers conduct an intensive 24-hour biological inventory, attempting to identify and record all species of living organisms in an area, while also educating the public about biodiversity.

The BioBlitz will happen at Rouge National Park which is a rather special kind of park due to it's proximity to the city of Toronto:

A wilderness area in Canada's largest city? That's right! Not too far from the skyscrapers of downtown Toronto, urban dwellers can see a different landscape where historic farms, century-old trees, peaceful meadows and lush wetlands await you at your transit stop.

Rouge Park is over 40 km2, protecting two National Historic Sites and a variety of ecosystems joining the post-glacial Oak Ridges Moraine, roughly 50 km north of Toronto, and the City's biggest wetland, where the Rouge River empties into Lake Ontario.

So, if a few of my readers are in the area, come out and join us for some collecting! 

Life in the freezer

Source: climatestate

The possibility that extreme life forms might exist in the lakes beneath the Antarctic ice sheet has fascinated scientists for decades. However, direct sampling of these lakes in the interior of Antarctica continues to present major technological challenges especially some of the them are covered with thick ice sheets. Recognising this, scientists from the British Antarctic Survey, and the Universities of Northumbria and Edinburgh have been searching around the retreating margins of the ice sheet for subglacial lakes that are becoming exposed for the first time since they were buried more than 100,000 years ago. This is because parts of the ice sheet are melting and retreating at unprecedented rates as the temperature rises at the poles due to global warming.

Credit: British Antarctic Survey

The researchers targeted Lake Hodgson on the Antarctic Peninsula which was covered by more than 400 m of ice at the end of the last Ice Age, but is now considered to be an emerging subglacial lake, with a thin layer of just 3-4 metres of ice. By using clean coring technologies they drilled through the ice in order to reach the sediments at the bottom of the lake. Samples were analysed with a variety of methods such as light microscopy, Fluorescence in Situ Hybridization (FISH), SEM, direct culture, and massive parallel sequencing. 

The lake was thought to be a harsh environment for any form of life but the layers of mud at the bottom of the lake represent a time capsule storing the DNA of the microbes which have lived there throughout the millennia. The top few centimetres of the core contained current and recent organisms which inhabit the lake but once the core reached 3.2 m deep the microbes found most likely date back nearly 100,000 years. Some of the life discovered was in the form of fossil DNA showing that many different types of bacteria live there, including a range of extremophiles which are species adapted to the most extreme environments. 

...the most numerous closest sequence matches were to both marine and soil derived organisms, many of which come from thermophilic environments. Although all were a relatively low fraction of the total, the two most abundant sequence matches were to marine bacteria that are found all over the world: Pirellula staleyi and Rhodopirellula baltica are globally distributed marine bacteria (the former a planctomycete which can also be found in terrestrial habitats). The second group of frequent matches were to the soil bacteria. Spirochaeta aurantia is an aerobe isolated from mud and Conexibacter woesei is a member of the Actinobacteria isolated from forest soil. The third group could be classified as an extremophile: Spirochaeta thermophila which is extremely thermophilic and marine, Thermobaculum terrenum from an extreme thermal soil and Leptospirillum ferrodiazotrophum was isolated from a subsurface acid mine drainage biofilm and is involved in iron oxidation. Further clues about the ecology of the environment could be derived from frequent sequence matches to Frankia—a genus of nitrogen fixing bacteria, Dehalococcoides ethenogenes—which is anaerobic and cannot use inorganic electron acceptors and Methylococcus capsulatus, a thermotolerant obligate methanotroph that is able to oxidize some organic hydrogen containing compounds...

However, only 77% of the DNA sequences identified could be matched to a known sequence, species or type strain, suggesting that a vast amount of biodiversity remains to be discovered. Many of the species are likely to be new to science making clean exploration of the remote lakes isolated under the deeper parts of the ice sheet even more pressing.

Life in the deep

The Lukina Jama-Trojama is the deepest cave system in Croatia, extraordinary for its vertical shape, long pits and great depth of -1392 m. From an ecological point of view this cave system is extremely interesting for having three microclimatic layers: first an entrance icy part with temperatures of about 1 °C followed by a middle part with temperatures up to 2 °C. The bottom part of the system shows higher temperatures up to 4 °C. These unusual living conditions make the cave extremely interesting for biodiversity research.

Now my colleague and friend Alexander Weigand has described a new species of the genus Zospeum from this cave system. The new species Zospeum tholussum is a small and fragile snail (1-2 mm), with a dome-like shaped translucent shell. Only one living specimen was found during an expedition around the galleries of the cave system. The animal was found at the remarkable depth of 980 m, in an unnamed chamber full of rocks and sand with a small stream running through it.

The species is related to Zospeum amoenum, but can be distinguished from the latter by some shell features and - as shown in the study as well - by DNA Barcoding.

All known species from the cave-dwelling genus Zospeum have only limited ability to move. Their preference for muddy habitats and the fact that they are usually located near the drainage system of the cave, in a close proximity to running water, however suggest that these animals are not exactly immobile. Scientists hypothesize that dispersal is achieved through passive transportation via water or larger mammals.

Orchids

Orchids are beautiful, fascinating flowers. There are over 25,000 species of orchids, and many are them are threatened, endangered or extinct, usually due to habitat destruction or poaching. Orchid smuggling is contributing to the loss of many species of orchid in the wild.

It is legal to trade in nursery-produced orchids. Orchid growers use artificial propagation and modern greenhouses that are capable of imitating the temperature, moisture, and wind conditions that orchids thrive upon in the wild. Nursery owners often outdo nature by producing plants superior to those found in the wild, healthier and with flowers that are larger and have more interesting colors.

For two reasons, orchid smuggling continues unabated. First of all, nursery-raised orchids are expensive. This is because it is time-consuming to raise orchids and the technology is not cheap. It is often cheaper, easier, and quicker to obtain orchids illegally from the wild. Because it is so much easier to collect orchids in the wild, smugglers often can undercut the prices of legitimate growers. Secondly, orchid collectors often find nursery-grown orchids to lack the exotic aura and mystery of wild orchids.

In Nepal for example wild orchids are illegally harvested and traded for use in local traditional medicine, horticulture, and international trade. Although the orchid trade has a long tradition, and illegal export to China, India and Hong Kong is rife there was no clear picture on the extend of the issue.

A new study now documents for the first time trade, species diversity, and traditional use of wild-harvested orchids in Nepal. The researchers did field surveys of markets and conducted interviews. Trade volumes and approximate income were estimated based on surveys and current market prices. Orchid samples were identified to species level using a combination of morphology and DNA Barcoding. The results are distressing:

Estimates show that 9.4 tons of wild orchids were illegally traded from the study sites during 2008/2009. A total of 60 species of wild orchids were reported to be used in traditional medicinal practices to cure at least 38 different ailments, including energizers, aphrodisiacs and treatments of burnt skin, fractured or dislocated bones, headaches, fever and wounds. 

That is just one area where illegal harvesting occurs. If one would extrapolate that on a global scale I am sure it would show an alarming picture about the status of orchids on our planet. The researchers in Nepal are taking it to the next level and make recommendations on alternatives that meet the demand and economic needs but still include proper conservation:

Collection of wild orchids was found to be widespread in Nepal, but illegal trade is threatening many species in the wild. Establishment of small-scale sustainable orchid breeding enterprises could be a valuable alternative for the production of medicinal orchids for local communities. Critically endangered species should be placed on CITES Appendix I to provide extra protection to those species. DNA barcoding is an effective method for species identification and monitoring of illegal cross-border trade.