Three new species of saddled loricariid catfishes, and a review of Hemiancistrus, Peckoltia, and allied genera (Siluriformes)

(Figs 2–4). CORBIDI 14685, an adult male (Figs 2–4) from 13.5806 S, 75.2449 W (WGS84), Chicchobamba, upstream of Represa Negrayccassa, upper drainage of the Huaytará river, 3900 m, Provincia Huaytará, Región Huancavelica, Peru, collected by A. Catenazzi, V. Vargas García, and M. Jaico Huayanay

We describe a new species of Telmatobius from the Pacific slopes of the Andes in central Peru. Specimens were collected at 3900 m elevation near Huaytará, Huancavelica, in the upper drainage of the Pisco river. The new species has a snout–vent length of 52.5 ± 1.1 mm (49.3–55.7 mm, n = 6) in adult females, and 48.5 mm in the single adult male. The new species has bright yellow and orange coloration ventrally and is readily distinguished from all other central Peruvian Andean species of Telmatobius but T. intermedius by having vomerine teeth but lacking premaxillary and maxillary teeth, and by its slender body shape and long legs. The new species differs from T. intermedius by its larger size, flatter head, and the absence of cutaneous keratinized spicules (present even in immature females of T. intermedius), and in males by the presence of minute, densely packed nuptial spines on dorsal and medial surfaces of thumbs (large, sparsely packed nuptial spines in T. intermedius). The hyper-arid coastal valleys of Peru generally support low species richness, particularly for groups such as aquatic breeding amphibians. The discovery of a new species in this environment, and along a major highway crossing the Andes, shows that much remains to be done to document amphibian diversity in Peru.

The Tropical Andes are characterized by a large diversification of the aquatic frogs of the genus Telmatobius Wiegmann, 1834. Sixty-two species are currently recognized in this genus (AmphibiaWeb 2014; Aguilar and Valencia 2009; Frost 2014; including species previously assigned to Batrachophrynus Peters, 1873). The altitudinal distribution of Telmatobius ranges from 1000 m to 5400 m (De la Riva and Harvey 2003; Seimon et al. 2007), and its longitudinal distribution extends from the equator (T. niger Barbour & Noble, 1920, whose populations have been extirpated in Ecuador; Merino-Viteri et al. 2005) to 29°S, on the eastern slopes of the Argentinean Andes (T. contrerasi Cei, 1977). Twenty-eight species of Telmatobius are distributed in Peru (Lehr 2005; AmphibiaWeb 2014), but of these only five [T. arequipensis Vellard, 1955; T. intermedius Vellard, 1955; T. jelskii (Peters, 1873); T. peruvianus Wiegmann, 1834; T. rimac Schmidt, 1954] are known to occur in the hyper-arid coastal valleys that drain directly into the Pacific Ocean.

During October 2012 we made several surveys for the Biodiversity and Monitoring Assessment Program of the Smithsonian Conservation Biology Institute’s Center for Conservation Education and Sustainability (Catenazzi et al. 2013a; Catenazzi et al. 2013b). During one of these surveys, we found a population of Telmatobius in the upper drainage of the Huaytará river (Region of Huancavelica), a tributary of the Pisco river in the Pacific slopes of the central Peruvian Andes. Individuals of this population possess traits that do not correspond to the morphological characteristics of other species found in the arid coastal valleys of central Peru (Fig. 1), namely T. rimac to the north and T. intermedius to the south (Vellard 1951; Schmidt 1954; Lehr 2005). Therefore, here we describe the new species and provide a diagnosis to differentiate it from congeneric forms.

Source: Read Full Artical at - zookeys

Quest continues for peanut that won't cause allergic reaction

Peanuts (stock image). Scientists must eliminate peanut allergens below a certain threshold for patients to be safe, said Wade Yang, an assistant professor in food science and human nutrition and member of UF’s Institute of Food and Agricultural Sciences. Credit: © yurakp / Fotolia

University of Florida scientist has moved one step closer to his goal of eliminating 99.9 percent of peanut allergens by removing 80 percent of them in whole peanuts.

Scientists must eliminate peanut allergens below a certain threshold for patients to be safe, said Wade Yang, an assistant professor in food science and human nutrition and member of UF’s Institute of Food and Agricultural Sciences.

If Yang can cut the allergens from 150 milligrams of protein per peanut to below 1.5 milligrams, 95 percent of those with peanut allergies would be safe. It’s challenging to eliminate all peanut allergens, he said, because doing so may risk destroying peanuts’ texture, color, flavor and nutrition. But he said he’s using novel methods like pulsed light to reach an allergen level that will protect most people.

Yang, whose study is published online in this month’s issue of the journal Food and Bioprocess Technology, cautioned that he has done peanut allergen experiments only in a laboratory setting so far. He hopes to eventually conduct clinical trials on animals and humans.

Dr. Shih-Wen Huang, professor emeritus in the Department of Pediatrics and Head of the Pediatric Allergy Clinic at UF Health, is familiar with the UF/IFAS research. Huang outlined more steps in the peanut allergen research.

The first is to see if the allergic antibody in the serum of peanut allergy patients will still bind with the residual allergy protein from the refined peanut products. The second is to see if the refined peanut extract would elicit skin-test reactions in peanut allergy patients.

The third step would be to conduct a double blind, placebo-controlled test to see if patients develop allergy symptoms after eating the refined products.

“I am pleased to see their work is progressing well,” Huang said. “However, more challenges are waiting until the final products are accepted from the public, especially the patients with peanut allergies.”

Two years ago, Yang was using his technique on peanut extract. He’s now testing it on the peanut itself. In his 2012 study, he removed up to 90 percent of the allergic potential from peanut protein extracts.

“This process proves that pulsed light can inactivate the peanut allergenic proteins and indicates that pulsed light has a great potential in peanut allergen mitigation,” Yang said.

About 1.9 million people, or 0.6 percent of U.S. residents, are allergic to peanuts, according to the National Institute of Allergy and Infectious Diseases, part of the National Institutes of Health.

Reactions can range from skin rashes to anaphylaxis, which can be fatal. Currently, the best way for those allergic to peanuts to stay safe is to avoid them, according to the NIH. Many people carry epinephrine injectors that help offset their allergy symptoms until they reach a hospital.

In the latest study, Yang and his colleagues applied the pulsed ultraviolet light technology to whole peanuts. That makes the findings more useful, because peanut processing usually starts from whole-peanut roasting, and roasted peanuts are then packaged to sell as whole peanuts or made into peanut butter, he said.

“The latest study moves one step closer to the actual production,” Yang said.

For the study, Yang used a pulsating light system – two lamps filled with xenon, two cooling blowers, one treatment chamber with a conveyor belt and a control module ─ to direct concentrated bursts of light to modify the peanut allergenic proteins. That way, human antibodies can’t recognize them as allergens and begin to release histamines.

Histamines create allergy symptoms such as itching, rashes and wheezing. The pulsing light reduced the allergenic potential of the major peanut proteins Ara h1-h3.

Source: University of Florida Institute of Food and Agricultural Sciences

Primates indispensable for regeneration of tropical forests

Moustached tamarins (Saguinus mystax) contribute crucially to the seed dispersal of the neotropical tree Parkia panurensis. Credit: Julia Diegmann

Primatologist and plant geneticists have studied the dispersal of tree seeds by New World primates.

Primates can influence seed dispersal and spatial genetic kinship structure of plants that serve as their food source. This is the result of a cooperation project of behavioral ecologist Eckhard W. Heymann from the German Primate Center (DPZ) with plant geneticists Birgit Ziegenhagen and Ronald Bialozyt from the Philipps-University Marburg. This study was funded by the German Research Foundation.

At the DPZ-field station Estación Biológica Quebrada Blanco in the Peruvian Amazonian lowlands, scientists studied how feeding, sleeping, and ranging habits of two species of New World monkeys affect the dispersal of the neotropical legume tree Parkia panurensis. For this, the researchers observed a group of Brown-mantled tamarins (Saguinus nigrifrons) and Moustached tamarins (Saguinus mystax), who jointly moved through home ranges in search of edible plants which included Parkia trees.

Fruits from these trees are pods that contain 16 to 23 seeds, each of which is surrounded by edible gum. The monkeys feed on the gum content of the pods and at the same time swallow the Parkia seeds which are later defecated intact in a different area.

During behavioral observations, researchers recorded the food intake of tamarins as well as the location of the Parkia trees that they visited. In addition, they collected faecal samples of the tamarins that contained seeds. "With the help of genetic analyses of the DNA found in the seed coat, which is of maternal origin, we could make an exact assignment of the corresponding "mother tree" for the seeds," says Eckhard W. Heymann from the DPZ. "This allowed us to determine how far Parkia seeds were dispersed by the monkeys."

In order to analyze the effect of seed dispersal by monkeys on a spatial genetic level, the scientists examined three different developmental stages of the trees. In addition to the seeds that contain the plant embryo, they collected leaves from young and mature Parkia trees in the home range of tamarins. "With the help of analysis from microsatellites, short repeated DNA sequences, we were able to identify genetic similarities of individual trees," says Heymann.

The analysis of the spatial genetic structure of the Parkia population revealed a significant genetic relationship of the plant embryos and young trees within a radius of 300 meters, which coincides with the distance within which most seeds are dispersed by the tamarins. For mature trees, the relationship was reduced to a radius of only up to 100 meters.

"In tropical rain forests, the seeds of 80 to 90 percent of trees and lianas are dispersed by animals. In addition to primates, birds and bats are the major animal groups that are responsible for seed dispersal," says behavioral ecologist Heymann. "For the plants, transport of their seeds is extremely important. As sedentary organisms, this is the only way that their offspring -- the embryos contained in the seeds -- can reach appropriate sites for germination and growth. Furthermore, this reduces the density-dependent mortality which occurs when the seeds fall under the mother plants," says Eckhard W. Heymann. Fruit-eating primates such as tamarins are therefore invaluable to the natural regeneration and diversity of ecosystems in which they live.

Source: German Primate Center

For tiger populations, a new threat

This is an Amur tiger photographed by camera trap. Credit: WCS Russia Program

Along with the pressures of habitat loss, poaching and depletion of prey species, a new threat to tiger populations in the wild has surfaced in the form of disease, specifically, canine distemper virus (CDV). According to a new study from the Wildlife Conservation Society (WCS) and its partners, CDV has the potential to be a significant driver in pushing the animals toward extinction.

While CDV has recently been shown to lead to the deaths of individual tigers, its long-term impacts on tiger populations had never before been studied.

The authors evaluated these impacts on the Amur tiger population in Russia's Sikhote-Alin Biosphere Zapovednik (SABZ), where tiger numbers declined from 38 individuals to 9 in the years 2007 to 2012. In 2009 and 2010, six adult tigers died or disappeared from the reserve, and CDV was confirmed in two dead tigers -- leading scientists to believe that CDV likely played a role in the overall decline of the population. Joint investigations of CDV have been an ongoing focus of WCS and Russian scientists at Sikhote-Alin Zapovednik and veterinarians at the regional Primorye Agricultural College since its first appearance in tigers in 2003.

A key finding of this study: Modeling shows that smaller populations of tigers were found to be more vulnerable to extinction by CDV. Populations consisting of 25 individuals were 1.65 times more likely to decline in the next 50 years when CDV was present. The results are profoundly disturbing for global wild tigers given that in most sites where wild tigers persist they are limited to populations of less than 25 adult breeding individuals.

The scientists used computer modeling to simulate the effects of CDV infection on isolated tiger populations of various sizes and through a series of transmission scenarios. These included tiger-to-tiger transmission and transmission through predation on CDV-infected domestic dogs and/or infected wild carnivores (such as foxes, raccoon dogs and badgers). High and low-risk scenarios for the model were created based on variation in the prevalence of CDV and the tigers' contact with sources of exposure.

Results showed that CDV infection increased the 50-year extinction probability of tigers in SABZ as much as 55.8 percent compared to CDV-free populations of equivalent size.

"Although we knew that individual tigers had died from CDV in the wild, we wanted to understand the risk the virus presents to whole populations," said WCS veterinarian Martin Gilbert. "Tigers are elusive, however, and studying the long-term impact of risk factors is very challenging. Our model, based on tiger ecology data collected over 20 years in SABZ, explored the different ways that tigers might be exposed to the virus and how these impact the extinction risk to tiger populations over the long term."

WCS Russia Program Director Dale Miquelle said, "Tigers face an array of threats throughout their range, from poaching to competition with humans for space and for food. 

Consequently, many tiger populations have become smaller and more fragmented, making them much more susceptible to diseases such as CDV. While we must continue to focus on the primary threats of poaching and habitat destruction, we now must also be prepared to deal with the appearance of such diseases in the future."

Priorities for future research, according to the authors, include identifying the domestic and wild carnivore species that contribute to the CDV reservoir, and those that are the most likely sources of infection for tigers. Tigers are too rare to sustain the virus in the long term, so CDV must rely on more abundant carnivore species to persist in the environment. 

Understanding the structure of the CDV reservoir will be a critical first step in identifying measures that might prevent or control future outbreaks. In addition, since we now know that small tiger populations are at greater risk to diseases such as CDV than larger populations, conservation strategies focusing on connectedness between populations become all the more important. "Estimating the potential impact of canine distemper virus on the Amur tiger population (Panthera tigris altaica) in Russia," appears in the current online edition of PloSONE. Authors include: Martin Gilbert of WCS and Boyd Orr Centre for Population and Ecosystem Health at the University of Glasgow; Dale G. Miquelle of WCS; John M. Goodrich of Panthera; Richard Reeve, Sarah Cleaveland and Louise Matthews of Boyd Orr Centre for Population and Ecosystem Health at the University of Glasgow; and Damien Joly of WCS and Metabiota.

This study was made possible through generous support from Morris Animal Foundation, Zoo Boise Conservation Fund, AZA Tiger Species Survival Plan Tiger Conservation Campaign, and the Biotechnology and Biological Sciences Research Council.

"Morris Animal Foundation is thankful to Dr. Miquelle and his team for helping protect the Amur Tigers," said Diane Brown, DVM, PhD, DACVP and Chief Scientific Officer for Morris Animal Foundation. "Our Foundation values their hard work and dedication to this study and we look forward to many more partnerships with the Wildlife Conservation Society."

Source: Wildlife Conservation Society

A kingdom of cave beetles found in Southern China

Credit: Mingyi Tian; CC-BY 4.0

A team of scientists specializing in cave biodiversity from the South China Agricultural University (Guangzhou) unearthed a treasure trove of rare blind cave beetles. The description of seven new species of underground Trechinae beetles, published in the open access journal ZooKeys, attests for the Du'an karst as the most diverse area for these cave dwellers in China.

"China is becoming more and more fascinating for those who study cave biodiversity, because it holds some of the most morphologically adapted cavernicolous animals in the world. This is specifically true for fishes and the threchine beetles, the second of which is also the group featured in this study," explains the senior author of the study Prof. Mingyi Tian.

Like most cavernicolous species, Trechinae cave beetles shows a number of specific adaptations, such as lack of eyes and colour, which are traits common among cave dwellers.

The new Trechinae beetles belong to the genus Dongodytes whose members are easily recognizable by their extraordinary slender and very elongated body. Members of this genus are usually very rare in caves, with only five species reported from China before now.

During the recent study of the cave systems in Du'an karst however this numbers drastically changed, Out of the 48 visited caves 12 held populations of trechine beetles. A total of 103 samples were collected, out of which the team of scientists determined ten different species, seven of which are new to science.

"This new discovery casts a new light on the importance of the Du'an Karst as a biological hotspot for cavernicolous Trechinae in China," adds Prof. Mingyi Tian.

Source: Pensoft Publishers

Seeing the forest for the trees: Youngest trees in a forest tell the biggest story

LSU ecologist Kyle Harms co-authors first study to quantify the process of diversification in forests and likely all other sessile ecosystems. Credit: Louisiana State University

The largest trees in a forest may command the most attention, but the smallest seedlings and youngest saplings are the ones that are most critical to the composition and diversity of the forest overall. While many people gaze up into the forest canopy, scientist Joseph Connell has spent much of his career looking down quite closely at the forest understory. Connell, who is a professor emeritus in the Department of Ecology, Evolution and Marine Biology at the University of California at Santa Barbara, established one of the world's longest, in-depth ecological research studies on the planet. The Connell Plots Rainforest Network has thus far produced a 50-year collection of data on individual trees in Australia's protected rainforests.

"Having such a long-term, detailed dataset is highly unusual. It's the kind of temporal depth we need to answer some of the big questions such as, what are the ecological processes that maintain diversity?" said Kyle Harms, professor in the LSU Department of Biological Sciences and a collaborator with Connell.

Early in his career, Harms was a post-doctoral researcher in Connell's lab at U.C. Santa Barbara. There, he met former fellow post-doctoral researcher and current collaborator Peter Green, who is a senior lecturer at La Trobe University in Melbourne, Australia.

Harms and Green were inspired to use their mentor's dataset; therefore, they devised an analysis to test the long-standing hypothesis that the patterns of composition and diversity among a forest's mature trees are largely set by processes that occur in trees' earliest life stages. Harms ran statistical analyses on 7,977 individual trees across 186 species that were censused in one of Connell's tropical Australian forest plots from 1971-2013.

He repeatedly ran simulation analyses on six tiers of trees based on size in order to predict the expected outcome of diversity at each tier. Then he compared the expected levels of diversity in each tier with the true collected data.

"What we found was that the seedlings are more diverse than the statistical expectations predicted them to be, but the larger trees' levels of diversity were about the same as the predictions" he said.

These results are the first quantitative evidence that the earliest life cycle stages of individual trees are more critical than later stages to the overall relative abundances of mature trees in a forest. Their findings will be published online in the Proceedings of the National Academy of Sciences this week.

The stronger influence of ecological sorting processes operating at the earliest life cycle stages compared to later life stages, which they quantified, also likely occurs in other highly diverse ecosystems with rooted, or sessile, organisms including grasslands, herbaceous plant communities and marine communities of coral.

"I think this is something that is happening broadly in ecosystems across the planet," Harms said.

He and his collaborators' results underscore the importance of support for long-term, in-depth datasets, as well as the need to investigate the early life stages -- for example, the smallest, newly germinated seedlings -- where the most critical processes are occurring.

"I think it helps us understand where to focus in order to really understand the biased sorting processes that create the composition and diversity patterns in the forest overall," he said.

Source: Louisiana State University

'Big Bang' of bird evolution mapped: Genes reveal deep histories of bird origins, feathers, flight and song

Crocodiles are the closest living relatives of birds, sharing a common ancestor that lived around 240 million years ago and also gave rise to the dinosaurs.
Credit: Stephen J. O'Brien, Avian Phylogenomics Group

The genomes of modern birds tell a story of how they emerged and evolved after the mass extinction that wiped out dinosaurs and almost everything else 66 million years ago. That story is now coming to light, thanks to an ambitious international collaboration that has been underway for four years.

The first findings of the Avian Phylogenomics Consortium are being reported nearly simultaneously in 29 papers -- eight papers in a Dec. 12 special issue of Science and 21 more in Genome Biology, GigaScience and other journals.

Scientists already knew that the birds who survived the mass extinction experienced a rapid burst of evolution. But the family tree of modern birds has confused biologists for centuries and the molecular details of how birds arrived at the spectacular biodiversity of more than 10,000 species is barely known.

To resolve these fundamental questions, a consortium led by Guojie Zhang of the National Genebank at BGI in China and the University of Copenhagen, Erich D. Jarvis of Duke University and the Howard Hughes Medical Institute and M. Thomas P. Gilbert of the Natural History Museum of Denmark, has sequenced, assembled and compared full genomes of 48 bird species. The species include the crow, duck, falcon, parakeet, crane, ibis, woodpecker, eagle and others, representing all major branches of modern birds.

"BGI's strong support and four years of hard work by the entire community have enabled us to answer numerous fundamental questions to an unprecedented scale," said Guojie Zhang. "This is the largest whole genomic study across a single vertebrate class to date. The success of this project can only be achieved with the excellent collaboration of all the consortium members."

"Although an increasing number of vertebrate genomes are being released, to date no single study has deliberately targeted the full diversity of any major vertebrate group," added Tom Gilbert. "This is precisely what our consortium set out to do. Only with this scale of sampling can scientists truly begin to fully explore the genomic diversity within a full vertebrate class."

"This is an exciting moment," said neuroscientist Erich Jarvis. "Lots of fundamental questions now can be resolved with more genomic data from a broader sampling. I got into this project because of my interest in birds as a model for vocal learning and speech production in humans, and it has opened up some amazing new vistas on brain evolution."

This first round of analyses suggests some remarkable new ideas about bird evolution. The first flagship paper published in Science presents a well-resolved new family tree for birds, based on whole-genome data. The second flagship paper describes the big picture of genome evolution in birds. Six other papers in the special issue of Science describe how vocal learning may have independently evolved in a few bird groups and in the human brain's speech regions; how the sex chromosomes of birds came to be; how birds lost their teeth; how crocodile genomes evolved; ways in which singing behavior regulates genes in the brain; and a new method for phylogenic analysis with large-scale genomic data.

The Avian Phylogenomics Consortium has so far involved more than 200 scientists hailing from 80 institutions in 20 countries, including the BGI in China, the University of Copenhagen, Duke University, the University of Texas at Austin, the Smithsonian Museum, the Chinese Academy of Sciences, Louisiana State University and many others.

A Clearer Picture of the Bird Family Tree
Previous attempts to reconstruct the avian family tree using partial DNA sequencing or anatomical and behavioral traits have met with contradiction and confusion. Because modern birds split into species early and in such quick succession, they did not evolve enough distinct genetic differences at the genomic level to clearly determine their early branching order, the researchers said. To resolve the timing and relationships of modern birds, the consortium authors used whole-genome DNA sequences to infer the bird species tree.

"In the past, people have been using 10 to 20 genes to try to infer the species relationships," Jarvis said. "What we've learned from doing this whole-genome approach is that we can infer a somewhat different phylogeny [family tree] than what has been proposed in the past. We've figured out that protein-coding genes tell the wrong story for inferring the species tree. You need non-coding sequences, including the intergenic regions. The protein coding sequences, however, tell an interesting story of proteome-wide convergence among species with similar life histories."

This new tree resolves the early branches of Neoaves (new birds) and supports conclusions about some relationships that have been long-debated. For example, the findings support three independent origins of waterbirds. They also indicate that the common ancestor of core landbirds, which include songbirds, parrots, woodpeckers, owls, eagles and falcons, was an apex predator, which also gave rise to the giant terror birds that once roamed the Americas.

The whole-genome analysis dates the evolutionary expansion of Neoaves to the time of the mass extinction event 66 million years ago that killed off all dinosaurs except some birds. This contradicts the idea that Neoaves blossomed 10 to 80 million years earlier, as some recent studies suggested.
Based on this new genomic data, only a few bird lineages survived the mass extinction. They gave rise to the more than 10,000 Neoaves species that comprise 95 percent of all bird species living with us today. The freed-up ecological niches caused by the extinction event likely allowed rapid species radiation of birds in less than 15 million years, which explains much of modern bird biodiversity.
Increasingly sophisticated and more affordable genomic sequencing technologies and the advent of computational tools for reconstructing and comparing whole genomes have allowed the consortium to resolve these controversies with better clarity than ever before, the researchers say.

With about 14,000 genes per species, the size of the datasets and the complexity of analyzing them required several new approaches to computing evolutionary family trees. These were developed by computer scientists Tandy Warnow at the University of Illinois at Urbana-Champaign, Siavash Mirarab, a student at the University of Texas at Austin and Alexis Stamatakis at the Heidelburg Institute for Theoretical Studies. Their algorithms required the use of parallel processing supercomputers at the Munich Supercomputing Center (LRZ), the Texas Advanced Computing Center (TACC) and the San Diego Supercomputing center (SDSC).

"The computational challenges in estimating the avian species tree used around 300 years of CPU time, and some analyses required supercomputers with a terabyte of memory," Warnow said.
The bird project also had support from the Genome 10K Consortium of Scientists (G10K), an international science community working toward rapidly assessing genome sequences for 10,000 vertebrate species.

"The Avian Genomics Consortium has accomplished the most ambitious and successful project that the G10K Project has joined or endorsed," said G10K co-leader Stephen O'Brien, who co-authored a commentary on the bird sequencing project appearing in GigaScience.

A Genomic Perspective of Avian Evolution and Biodiversity
For all their biological intricacies, birds are surprisingly light on DNA. A study led by Zhang, Cai Li and the consortium authors found that compared to other reptile genomes, avian genomes contain fewer of the repeating sequences of DNA and lost hundreds of genes in their early evolution after birds split from other reptiles.

"Many of these genes have essential functions in humans, such as in reproduction, skeleton formation and lung systems," Zhang said. "The loss of these key genes may have a significant effect on the evolution of many distinct phenotypes of birds. This is an exciting finding, because it is quite different from what people normally think, which is that innovation is normally created by new genetic material, not the loss of it. Sometimes, less is more."

From the whole chromosome level to the order of genes, this group found that the genomic structure of birds has stayed remarkably the same among species for more than 100 million years. The rate of gene evolution across all bird species is also slower compared to mammals.

Yet some genomic regions display relatively faster evolution in species with similar lifestyles or phenotypes, such as involving vocal learning. This pattern of what is called convergent evolution may be the underlying mechanism that explains how distant bird species evolved similar phenotypes independently. Zhang said these analyses on particular gene families begin to explain how birds evolved a lighter skeleton, a distinct lung system, dietary specialties, color vision, as well as colorful feathers and other sex-related traits.

Important Lessons

The new studies have shed light on several other questions about birds, including:
How did vocal learning evolve?  Eight studies in the package examined the subject of vocal learning. According to new evidence in the two flagship papers, vocal learning evolved independently at least twice, and was associated with convergent evolution in many proteins. A Science study led by Andreas Pfenning, Alexander Hartemink, Jarvis and others at Duke, in collaboration with researchers at the Allen Institute for Brain Science in Seattle and the RIKEN Institute in Japan, found that the specialized song-learning brain circuitry of vocal learning birds (songbirds, parrots and hummingbirds) and human brain speech regions have convergent changes in the activity of more than 50 genes. Most of these genes are involved in forming neural connections. Osceola Whitney, Pfenning and Anne West, also of Duke, found in another Science study that singing is associated with the activation of 10 percent of the expressed genome, with diverse activation patterns in different song-learning regions of the brain, controlled by epigenetic regulation of the genome. Duke's Mukta Chakraborty and others found in a PLoS ONE study that parrots have a song system within a song system, with the surrounding song system unique to them. This might explain their greater ability to imitate human speech. In a BMC Genomics study, Morgan Wirthlin, Peter Lovell and Claudio Mello from Oregon Health & Science University found unique genes in the song-control brain regions of songbirds.

The XYZW of sex chromosomes. Just as the sex of humans is determined by the X and Y chromosomes, the sex of birds is controlled by the Z and W chromosomes. The W makes birds female, just as the Y makes humans male. Most mammals share a similar evolutionary history of the Y chromosome, which now contains many degenerated genes that no longer function and only a few active genes related to "maleness." A Science study led by Qi Zhou and Doris Bachtrog from the University of California, Berkeley, and Zhang found that half of bird species still contain substantial numbers of active genes in their W chromosomes. This challenges the classic view that the W chromosome is a "graveyard of genes" like the human Y.

This group also found that bird species are at drastically different states of sex chromosome evolution. For example, the ostrich and emu, which belong to one of the older branches of the bird family tree, have sex chromosomes resembling their ancestors. Yet some modern birds such as the chicken and zebra finch have sex chromosomes that contain few active genes. This opens a new set of questions on how the diversity of sex chromosomes may drive the diversity of sex differences in the outward appearance of various bird species. Peacocks and peahens are dramatically different; male and female crows are indistinguishable.

How did birds lose their teeth? In a Science study led by Robert Meredith from Montclair State University and Mark Springer from the University of California, Riverside, a comparison between the genomes of living bird species and those of vertebrate species that have teeth identified key mutations in the parts of the genome that code for enamel and dentin, the building blocks of teeth. The evidence suggests that five tooth-related genes were disabled within a short time period in the common ancestor of modern birds more than 100 million years ago.

What's the connection between birds and dinosaurs? Unlike mammals, birds (along with reptiles, fish and amphibians) have a large number of tiny microchromosomes. These smaller packages of gene-rich material are thought to have been present in their dinosaur ancestors. A study of genome karyotype structure in BMC Genomics analyzed whole genomes of the chicken, turkey, Peking duck, zebra finch and budgerigar. It found the chicken has the most similar overall chromosome pattern to an avian ancestor, which was thought to be a feathered dinosaur. This work was led by Darren Griffin and Michael Romanov from the University of Kent, and by Dennis Larkin and Marta Farré from the Royal Veterinary College, University of London.

Another study in Science examined birds' closest living relatives, the crocodiles. This team, led by Ed Green and Benedict Paton from the University of California, Santa Cruz, David Ray from Texas Tech University and Ed Braun from the University of Florida, found that crocodiles have one of the slowest-evolving genomes. The researchers were able to infer the genome sequence of the common ancestor of birds and crocodilians (archosaurs) and therefore all dinosaurs, including those that went extinct 66 million years ago.

Do differences in gene trees versus species trees matter? In the phylogenomics flagship study by Jarvis and others, the consortium found that no gene tree has a history exactly the same as the species tree, partly due to a process called incomplete lineage sorting. Another Science study, led by Tandy Warnow at the University of Texas and the University of Illinois, and her student Siavash Mirarab, developed a new computational approach called "statistical binning." They used this approach to show it does not matter much that the gene trees differ from the species tree because they were able to infer the first coalescent-based, genome-scale species tree, combining gene trees with similar histories to accurately infer a species tree.

Do bird genomes carry fewer virus sequences than other species? Mammalian genomes harbor a diverse set of genomic "fossils" of past viral infections called "endogenous viral elements" (EVEs). A study published in Genome Biology led by Jie Cui of Duke-NUS Graduate Medical School in Singapore, Edward Holmes of the University of Sydney and Zhang, found that bird species had 6-13 times fewer EVE infections in their past than mammals. This finding is consistent with the fact that birds have smaller genomes than mammals. It also suggests birds may either be less susceptible to viral invasions or better able to purge viral genes.

When did colorful feathers evolve? Elaborate, colorful feathers are thought to be evolutionarily advantageous, giving a male bird in a given species an edge over his competitors when it comes to mating. Zhang's flagship paper in Science, which is further analyzed by Matthew Greenwold and Roger Sawyer from the University of South Carolina in a companion study in BMC Evolutionary Biology, found that genes involved in feather coloration evolved more quickly than other genes in eight of 46 bird lineages. Waterbirds have the lowest number of beta keratin feather genes, landbirds have more than twice as many, and in domesticated pet and agricultural bird species, there are eight times more of these genes.

What happens to species facing extinction or recovering from near-extinction? Birds are like the proverbial canaries in the coal mine because of their sensitivity to environmental changes that cause extinction. In a Genome Biology study led by Shengbin Li, Cheng Cheng and Jun Yu from Xi'an Jiaotong University and Jarvis, researchers analyzed the genomes of species that have recently gone nearly extinct, including the crested ibis in Asia and the bald eagle in the Americas. They found genes that break down environmental toxins have a higher rate of mutations in these species and there is lower diversity of immune system genes in endangered species. In a recovering crested ibis population, genes involved in brain function and metabolism are evolving more rapidly. The researchers found more genomic diversity in the recovering population than was expected, giving greater hope for species conservation.

The Start of Something Bigger
This sweeping genome-level comparison of an entire class of life is being powered by frozen bird tissue samples collected over the past 30 years by museums and other institutions around the world. Samples are sent as fingernail-sized chunks of frozen flesh mostly to Duke University and University of Copenhagen for DNA separation. Most of the genome sequencing and critical initial analyses of the genomes have then been conducted by the BGI in China.

The avian genome consortium is now creating a database that will be made publicly available in the future for scientists to study the genetic basis of complex avian traits.

Setting up the pipeline for the large-scale study of whole genomes -- collecting and organizing tissue samples, extracting the DNA, analyzing its quality, sequencing and managing torrents of new data -- has been a massive undertaking. But the scientists say their work should help inform other major efforts for the comprehensive sequencing of vertebrate classes. To encourage other researchers to dig through this 'big data' and discover new patterns that were not seen in small-scale data before, the avian genome consortium has released the full dataset to the public in GigaScience, and in NCBI, ENSEMBL and CoGe databases.

Under the leadership of Dave Burt, the National Avian Research Facility at the Roslin Institute and Edinburgh University, UK, has created genome browser databases based on the ENSEMBL model for 48 species.

Source: Duke University

The Loss of biodiversity limits toxin degradation

You might not think of microbes when you consider biodiversity, but it turns out that even a moderate loss of less than 5% of soil microbes may compromise some key ecosystem functions and could lead to lower degradation of toxins in the environment.

Research published today in the SfAM journal, Environmental Microbiology, reports that without a rich diversity of soil bacteria, specialized functions such as the removal of pesticide residues are not as effective.

Dr Brajesh Singh of the University of Western Sydney led the work, he said "If the ability of the ecosystem to remove toxins from the environment is reduced, there will be higher toxicity risks in the environment and for non-target organisms, including humans, from agricultural chemicals. It is likely that these contaminants will remain at higher levels in surface and underground water, as well. It is vital to gain a better understanding of the extent to which soil bacteria are involved in the removal of contaminants."

The reasons for, and extent of, the decline in microbial diversity in agricultural soils is likely to be complex. The team has looked specifically at long-term heavy metal pollution where metals such as cadmium, zinc, and copper build up in the environment, usually as a result of industrial use. Another source is from digested sewage sludge, which is spread in agriculture fields to supply nutrients to crops and improve soil fertility; the sludge has historically contained some heavy metals, which can become concentrated in the soil.

Although the concentration of heavy metal used this study was higher than the current EU limit, this study has confirmed that long-term exposure to such contaminants does reduce the diversity of bacteria in the soil.

With the global population set to reach nine billion by 2050, we face a challenge to feed an extra two billion mouths using the same resources that we have at present. Crop losses to pests and disease account for a large percentage of under-production and so giving up pesticides will be difficult. Similarly, the use of sludge as a fertilizer is likely to become more prevalent. Research like this allows us to understand better how to use important agrichemicals and waste products in a sustainable way and so will contribute to future food and environmental security.

Source: Wiley

The Philippine tarsier: Genetic proof of a new variety

It’s not a monkey. It’s not a lemur. It’s not an African Bush Baby or even a Madagascan Mouse. Meet the Philippine tarsier: a tiny, adorable and downright “cool” primate from Southeast Asia. Credit: Image courtesy of University of Kansas

It's not a monkey. It's not a lemur. It's not an African Bush Baby or even a Madagascan Mouse. Meet the Philippine tarsier: a tiny, adorable and downright "cool" primate from Southeast Asia.

"It's really not like any animals that Americans are familiar with," said Rafe Brown, curator-in-charge at the University of Kansas' Biodiversity Institute. "A tarsier has giant eyes and ears; an extremely cute, furry body; a long tail with a furry tuft at the end; and interesting expanded fingers and toe tips that look a bit like the disks on the digits of tree frogs."

Brown said the tarsier (tar-SEER) has become the "flagship" iconic species for promoting environmental stewardship and ecotourism in the Philippines, a nation suffering from large-scale destruction of natural habitat.

"They're threatened with habitat loss due to development, mining and deforestation from the timber industry," Brown said. "On Bohol, where they are a big part of the tourist economy, literally thousands of animals are taken out of the wild, essentially harassed by tourists, and die in captivity due to the stress and inability of their captors to feed them an appropriate diet of live small animals. Tarsiers must eat an enormous amount every night to fuel their high metabolism."

Because of threats to the tarsier, conservation efforts are mounting for the charismatic animal. But these have been thwarted by a lack of research: Too little has been known about the tarsier's taxonomic diversity; there have been too few field studies; and a scarcity of genetic samples and voucher specimens in biodiversity repositories has left advocates of the tarsier in the dark. In short, to save the tarsier, experts have needed to know much more about the species.

"Basically, we can not legally protect something if we do not know that it exists," Brown said.
Today, research by Brown and colleagues published by the journal PLOS ONE will shed new light on the animal's genetic diversity and distribution. Additionally, the KU researchers have verified the presence of a new variety of tarsier, one heretofore only suspected to exist -- the Dinagat-Caraga tarsier.

"Previously tarsiers were one species, divided into three named subspecies," Brown said. "Our data disagree with that subspecies arrangement and instead demonstrate that the Philippine tarsiers are divided into three genetic units -- but these units are from different localities than the named taxa. So our data provide an objective way to restructure conservation efforts and point the resources where they need to go, in order to really have an effective impact on preserving genetic diversity in the group."

Brown's student Anthony Barley performed genetic sequencing of the tarsiers' mitochondrial DNA at KU, while fellow student Karen Olsen characterized the nuclear microsatellite loci variation of the animals.

According to Brown, the results "tell us that we need a protected area -- such as a national park -- in the ranges of each of the genetic units if our goal is to maximally preserve the genetic underpinnings of that biodiversity. Currently, the newly discovered entity, the Dinagat-Caraga tarsier, has no protection. It is known from a small island that is being extremely heavily mined. Thus, it emerges as a new lineage -- and a new major conservation urgency."

They question of just how many Philippine tarsiers exist has been "left sort of hanging" for 25 years until now, according to the researcher. The newly discovered Dinagat Island and Caraga Region tarsier was first recognized as possibly distinct by the Filipino biologist Dioscoro Rabor in the 1970s, and now is confirmed by the KU genetic analysis.

"The confirmation of Rabor's early suspicions about the Dinagat Island tarsier population was extremely exciting, and it was very satisfying to affirm his very perceptive early observations," Brown said. "He commented that it looked larger to him and had different shaped fingers and toes. I'm just glad we were able to bring new, modern tools to this problem and identify the Dinagat-Caraga tarsier as a real conservation priority."

Brown and Filipino colleagues have called for the establishment of separate tarsier sanctuaries and protection programs within the range of "at least" the three genetic entities established by the research at the Biodiversity Institute. Each, he said, merits unique strategies and programs, along with identification and remediation of conservation threats -- for instance "mining in Dinagat versus unregulated tourist industry on Bohol," he said.

To do less, Brown said, would harm the tarsier's long-term prospects, potentially depriving the Philippines and the rest of the world of one of nature's most charming and curious mammals.

"They move very rapidly and jump from tree trunk to tree trunk with 'ricochet locomotion,'" Brown said. "They bounce from small sapling trunk to trunk, then leap down to pounce on their prey. They're completely carnivorous. This is relatively unique among primates. The tarsier is famous for not eating any vegetable material of any kind. They eat insects, small snakes, lizards, small mammals and birds. They communicate with ultrasonic calls outside the range of human hearing. The tarsier is so cool!"

Source: University of Kansas