College of Agriculture and Life Sciences

Texas A&M Researcher Uses Genes to Map Evolution of Species

COLLEGE STATION – Genes, whether from apes or the trees they live in, are the storytellers of the origins of a species, according to a Texas A&M University ecosystem science and management assistant professor in College Station.

Dr. Claudio Casola, in his first year at Texas A&M as a forest genomicist, analyzes large molecular data sets — mainly DNA sequences of genomes — to determine patterns of gene evolution.

Casola said genes are DNA strings containing the basic information to build and maintain cells, tissues and essentially the whole organism. And, his interest is in understanding the specific role of each gene and how the genes in different species originated and function – regardless of species.

Recently, his research on DNA was included in articles being published in two different journals, Nature and Nature Genetics.

Dr. Claudio Casola, a Texas A&M University ecosystem science and management assistant professor

Dr. Claudio Casola is a Texas A&M University ecosystem science and management assistant professor.

The two articles describe the sequencing and analysis of several primate genomes. The Nature paper concerns gibbons, while the Nature Genetics paper is about the common marmoset, a small South American monkey important to biomedical research.

While he has published and presented research focused on a variety of genomic analyses of animals, plants and fungi genomes, Casola’s current position is specifically aimed at understanding the genetics and genomics of pine trees and other economically and ecologically relevant tree species, especially in the U.S. and Texas.

While not directly related to his current work, the research Casola conducted for these papers is very similar to what he is doing now in relation to forest trees.

“In fact, my work for these two studies was aimed at finding gene duplications and gene losses across these and other primates, including humans,” he said.

Casola said ‘gene duplication’ is the process that makes genes more abundant and is a major driver of evolution and species diversity.

“I take advantage of public databases of DNA information in genome sequences or the complete DNA information of a species, which is currently available for a number of organisms. I also generate my own genomic data sets whenever possible or needed.

“A key aspect of my work is the comparative analysis of gene data,” he said. “By looking at what genes have become more abundant or have been lost in a species compared to another species, I can infer the molecular basis of some biological differences between these species.”

Cover page of Nature magazine featuring the "Gibbon genome and the fast karyotype evolution of small apes" article

Dr. Casola’s research on DNA was featured in Nature magazine, describing the sequencing and analysis of several primate genomes.

The studies on the gibbons and marmoset genomes are the result of large collaborations involving several labs in the U.S. and other countries, Casola said. The main goals of both works include improving the general knowledge of these primate genetics and genomics to better understand human evolution, human biology and the molecular causes of human diseases.

“Improving our knowledge of the biology of these animals and providing better molecular tools for conservation purposes of endangered species are other fundamental aims of these projects,” he said.

Gibbons, also known as lesser apes, evolved a combination of anatomical features that allow them to swing at high speed from branch to branch for distances up to 50 feet. They also have experienced a uniquely high level of chromosomal breaks and fusions among primates that possibly accelerated the speciation process in this group.

Casola said 19 known gibbon species represent three-quarters of all ape species.

In the Nature article, the team presents the genome assembly for a female northern white-cheeked gibbon, he said. They uncovered a group of gibbon-specific retrotransposons—short DNA sequences able to make many copies of themselves that eventually ‘attach’ somewhere in the genome—that could be implicated in chromosomal reshuffling experienced by gibbons.

The genome of primates, including humans, host millions of retrotransposon copies. However, the gibbon-specific retrotransposons known as LAVA elements might have disrupted the activity of some genes involved in chromosomal organization, he explained.

“Interestingly, my comparative analysis of primate genomes shows that in contrast to the high chromosomal rearrangement levels, gene duplications and gene losses have not been particularly elevated in gibbons,” Casola added. “This finding suggests that whatever process is responsible for the chromosomal rearrangements, it did not speed up gene turnover.”

He performed a similar analysis in the common marmoset, a species in which females often give birth to dizygotic twins.

“In my work on the common marmoset genome, I identified hundreds of gene duplication and loss events that have occurred in the past 40 million years. At the same time, studying this genome allowed me to find several genes that have been lost during the evolution of humans, but are still present in this monkey and other mammals,” Casola said.

Dissecting the genome organization and gene evolution of pine trees will be more challenging than in primates, he said.

“Pine tree genomes contain between 20-35 billion bases, or ‘letters,’ which is seven to 11 times the size of our own genome. In other words, they are much more difficult to decode,” Casola said. “However, several pine tree and spruce genomes have already been sequenced, including the loblolly pine tree, which is the primary commercial forest species in the Southeastern United States. This will have a great impact on the genetics research in these species.”

Casola said his research is already taking advantage of these resources, and is also focusing on improving the sequence of the loblolly pine genome.

“Even after sequencing a genome you always end up having lots of short sequences that are very hard to put together,” he said. “One of my goals is to find better ways to join these pieces by working with other researchers at Texas A&M University, the Texas A&M Forest Service and the USDAForest Service Southern Research Station,” he said.

This effort will be important to develop genetic tools that can help improve the wood quality of commercial pine trees, and potentially obtain trees more resistant to drought and pests through breeding, Casola said.

“I’ve always enjoyed digging into genomic data to find out how genes and species evolved,” he said. “Now I can apply this information to understand how pine trees adapted to their environment, and hopefully this will translate into tools that can help contain the effects of climate change on some of our forests.”

Links to both of the journal articles can be found on Casola’s website under the Publications tab.

This article was originally published in AgriLife Today.

You can support faculty research in Texas A&M University’s College of Agriculture and Life Sciences with a gift of endowment to the Texas A&M Foundation.

Steve Blomstedt ’83
Senior Director of Development

College of Agriculture and Life Sciences
(979) 845-9582

A Promise Made Will Be a Promise Paid

Everyone who grows up in Texas knows that at some point, there comes a choice: Aggie or longhorn.
“Half my peers went one way, half the other, and for some reason I chose Aggie,” said Charles Manning ’82, who came to Texas A&M University in 1978 and graduated a year early with a degree in finance.

M. Ann and Charles Manning '82

M. Ann and Charles Manning ’82

“I remember walking around campus, seeing names on buildings and reading about former student benefactors, and I vowed to myself that I would join their ranks if circumstances allowed,” he said.

Flash forward to today, where his promise is set to be fulfilled. In a tremendous philanthropic gesture, Charles and his wife Ann solidified a significant planned gift through the Texas A&M Foundation to benefit four Texas A&M entities: Mays Business School, the College of Agriculture and life Sciences, the College of Veterinary Medicine and Biomedical Sciences, and the 12th Man Foundation.

Thoughtful Planning
With hefty retirement accounts and no children, the Mannings wanted to plan for the final distribution of their estate in a tax-efficient way. They worked closely with their attorney, Amy Bloomquist ’83, to create a giving strategy that is now documented in their estate plan. In addition to a generous bequest planned in their living trust, they have named the Texas A&M Foundation as a beneficiary of their retirement accounts after their lifetimes.
“Retirement account assets are not very tax-friendly, so a planned gift was an easy decision,” said Charles. With both gifts, the Mannings will hold, manage, enjoy and continue to build their estate during their lifetimes, and Texas A&M will benefit greatly.

They designed all of their endowments to allow college deans maximum flexibility in the use of funds.
“I have no idea what the needs of each college will be in 20, 30 or 40 years, but I do trust that the deans will be good stewards of these funds,” said Charles, who chose each beneficiary with care.

Banking Reaps Benefits
Retired now and living in Austin, the Mannings enjoyed productive and fruitful careers. Charles worked in banking technology, writing software used by banks nationwide. Ann received a juris doctor degree from Ohio northern University and originally worked for a law practice.

A Spirit Worth Preserving
Mays Business School Dean Jerry Strawser says the Mannings’ gift will impact students in countless ways.“With the flexibility they are allowing, it can support student scholarships, study abroad opportunities, student travel competitions and faculty teaching and research activities,” he said.

During a recent conversation, Dean Eleanor Green of the College of Veterinary Medicine and Biomedical Sciences told the Mannings that private gifts keep the spirit of Texas A&M a reality.

“She reminded us that cultures must be nurtured and that giving resources to the right people can generate a culture and spirit worth preserving,” said Charles.

By Dunae Crenwelge ’15

This article was originally posted in the Legacy section of the summer 2014 issue of Spirit magazine. Read the full publication here.

You can support the Mays Business School with a gift of endowment to the Texas A&M Foundation.

Brian Bishop ’91
Senior Director of Development

(979) 862-3615

Protecting the Red Sea’s Coral Reefs

The Red Sea is home to some of the world’s few remaining pristine coral reefs. These reefs are not only beautiful, but also extremely diverse with close to 300 species of hard coral recorded throughout the Red Sea. Of the 1,200 or so species of fish that call these reefs home, about 10% are found nowhere else.

Nevertheless, with population growth along the coasts, the health of these coral reefs, especially those along the Saudi Arabia border, may be in jeopardy. Fortunately, Dr. Daniel Roelke, a Professor of Wildlife and Fisheries Sciences with support through the Institute of Applied Mathematics and Computational Biology at Texas A&M University, is partnering with faculty at Saudi Arabia’s King Abdullah University of Science and Technology (KAUST) to ensure the safety of these reefs as well as the marine biota living on and within the reefs.

Impacts of Development Along the Red Sea

Saudi Arabia is traditionally known for an economy based in petroleum oils. In 2005, however, Abdullah bin Abdulaziz Al Saud, the king of Saudi Arabia, announced a megaproject to diversify the country’s economy. As a result of this megaproject, the coast along the Red Sea has since become more industrialized, rapidly increasing the population living in this area.Saudi-Arabia-map-300x294

As the population along the coast rises, the need for more freshwater and food production follows suit. To meet this need, desalinization plants and fisheries have popped up all long the Red Sea coastline.

An increase in desalinization, the process by which salt water is turned into freshwater suitable for human consumption, and aquaculture activities are directly impacting water circulation and the balance of nutrients within the water, potentially harming the coral reefs.

Brine, the by-product of the desalinization process, contains many concentrated chemicals. “Although the brine is usually disposed of in wells or discharged in the ocean with regulations, in many cases the regulation lacks monitoring and enforcement,” said Dr. Roelke. “Areas of coastal oceans that have restricted circulation, such as shallow regions between fringing reefs and the shoreline, are most susceptible to the toxic effects of brine discharge.”

The increased aquaculture activities along the coast have also led to an overflowing of water containing feed wastage, chemicals from animal excretion, and fecal material. This polluted water significantly contributes to the nutrient loading of the Red Sea, affecting the growth of phytoplankton, photosynthesizing microscopic organisms.

Phytoplankton Interactions

Phytoplankton inhabit the upper sunlit layer of almost all oceans and bodies of water, controlling the amount of light that reaches organisms below the water’s surface, such as coral reefs.

These plankton communities are sensitive to both nutrient loadings and changes in the depth of vertical water mixing, which can affect phytoplankton biomass. Nitrogen and phosphorus, both prevalent during nutrient loading, increase phytoplankton growth, shifting the composition of the phytoplankton assemblages. Since phytoplankton biomass and composition influence light level at varied wavelengths, the shift in composition can lead to significant shifts in the spectral quality of the underwater light field.

“Though it is uncertain how this shift in spectral quality will affect the coral reefs long-term, it is known that reefs are influenced by the magnitude and quality of light available to them,” said Dr. Roelke. “For example, coral populations acclimated at one depth do not perform as well when moved to another depth.”

Through a combination of numerical modeling, in-field experimentation, and monitoring, Dr. Roelke and his colleagues at KAUST are working to better understand the relationships among nutrient loading, mixing depth, phytoplankton biomass and composition, and spectral quality of light incident upon the coral reefs of the Red Sea. 

Border Impacts

This research will undoubtedly have a major influence on the health of the coral reefs, however, there are broader impacts of this partnership research project.

The research team, which includes Dr. Jay Walton, a Professor of Mathematics and Aerospace Engineering at Texas A&M University, and several faculty members from KAUST, is dedicated to the advancement of women in the STEM fields. “By recruiting and advancing women graduate students with computational training,” Dr. Roelke said, “our research will broaden participation of an underrepresented group in the discipline of quantitative ecology.”

Dr. Daniel Roelke with graduate student Frances Withrow on the KAUST campus. Photo courtesy of Dr. Roelke.

Dr. Daniel Roelke with graduate student Frances Withrow on the KAUST campus. Photo courtesy of Dr. Roelke.

Dr. Roelke’s graduate student Frances Withrow, a masters student enrolled in a joint degree program with Wildlife and Fisheries Sciences and the Peace Corps, has already played a significant role in developing the model that will be used in further Red Sea research. She has presented these findings at professional conferences in New Orleans, Honolulu and Saudi Arabia.

Because of the partnership with KAUST, this research project will also help to lower cultural barriers between non-Muslims and Muslims. “One way to counter cultural stigmatization is to increase the personal interactions between people of varied cultural backgrounds,” added Dr. Roelke. “This research project offers an excellent opportunity for this level of interaction, since much of the research will be coordinated at KAUST, an academic environment that is quite diverse.”

KAUST’s faculty and student population come from more than 60 nationalities from around the world. It is planned that graduate students involved in this research project will live at KAUST for a period, where they will receive international mentoring, enroll in classes, and participate in workshops and seminars. They will be immersed in an environment filled with opportunities for personal multicultural interactions.

“This research stretches beyond protecting our environment,” said Dr. Roelke. “It’s exciting to be a part of a project that is empowering students at Texas A&M University and KAUST to reach across cultural boundaries to save the Red Sea coral reefs, one of world’s most beautiful treasures.”

This article was originally published by the College of Agriculture and Life Sciences.

You can support faculty research at Texas A&M University’s College of Agriculture and Life Sciences with a gift of an endowment to the Texas A&M Foundation.


Steve Blomstedt ’83
Senior Director of Development
(979) 845-9582

Texas A&M study: Bioenergy sorghum could help with greenhouse gas emissions

COLLEGE STATION – Bioenergy sorghum may offer more than another energy supply; it may offer a “sink” for greenhouse gases, according to a Texas A&M AgriLife Research study.

Dr. Joe Storlien in biomass sorghum about six weeks before harvest.

Dr. Joe Storlien in biomass sorghum about six weeks before harvest.

Researchers in the Texas A&M University soil and crop sciences department have been measuring greenhouse gases from biofuel production scenarios to help quantify the carbon footprint of a bioenergy cropping system and evaluate compliance with federally mandated reduction goals.

The study, “Impacts of Biomass Sorghum Feedstock Production on Carbon Sequestration and Greenhouse Gas Emissions,” was funded by the AgriLife Research Cropping Systems bioenergy program and a U.S. Department of Agriculture-National Institute of Food and Agriculture grant.

Dr. Frank Hons, professor of soil science and AgriLife Research Faculty Fellow; Dr. Joe Storlien, postdoctoral research associate; Dr. Jason Wight, assistant research scientist; and Dr. James Heilman, professor of environmental physics, jointly worked on the research.

Hons explained that bioenergy sorghum may play a significant role in future biofuel production as a high quality biomass feedstock. To date, no studies have quantified life cycle greenhouse gases from this source.

“Bioenergy crop production represents an opportunity for greenhouse gas mitigation in the U.S.,” said Hons. “Crop production systems can be a net sink or net source of atmospheric carbon dioxide, depending on a number of factors, including land management practices.”

Life cycle analyses are used to evaluate biofuel efficiency by balancing the direct and indirect greenhouse gases associated with production with the total energy output and soil carbon storage, said Storlien.

One objective of their study was to determine the effects of crop rotation, nitrogen fertilization and residue management on net greenhouse gas emissions from bioenergy sorghum production. The study analyzed direct and indirect greenhouse emissions, soil carbon sequestration to a 3-foot depth, and theoretical biofuel yield from eight different bioenergy sorghum production scenarios.

Dr. Joseph Storlein measuring greenhouse gas emissions in biomass sorghum.

Dr. Joseph Storlein measuring greenhouse gas emissions in biomass sorghum.

The study centered on a field near College Station under bioenergy sorghum production since 2008. The researchers collected soil samples prior to the start of the study and each following spring in order to study changes in soil carbon storage and nutrient availability over time.

Annual accrual rates of soil organic carbon were much higher than anticipated, ranging from 1.2 to 3.3 tons of carbon per acre across all treatment combinations, Wight said. The corn-sorghum sequence had a significantly lower annual accrual rate than monoculture sorghum.

The high carbon sequestration rates from sorghum may be attributed to the high yield potential, more than 20 dry tons per acre, and the fact that the study was conducted in carbon-depleted soil, Storlien said. Moderate and severe drought conditions in 2010 and 2011 may also have contributed to soil organic carbon accrual if greater carbon production was allocated to roots scavenging for water.

Unfertilized, monoculture sorghum with half the yield returned to the field to provide nutrients and organic matter had the greatest overall biofuel production efficiency based on net greenhouse gas emissions savings, he said. However, crop rotation and fertilization would be recommended to minimize pest pressure and sustain long-term crop yield.

“These results have significant implications for net greenhouse gas emissions, soil organic carbon sequestration and life-cycle analyses,” Hons said. “Few studies have quantified greenhouse gas emissions and below-ground carbon inputs from bioenergy sorghum, and further investigation is warranted.”

This article was originally posted in Texas A&M AgriLife Today.

You can support faculty research at Texas A&M University’s College of Agriculture and Life Sciences with a gift of an endowment to the Texas A&M Foundation.


Steve Blomstedt ’83
Senior Director of Development
(979) 845-9582

Tiny, Tenacious and Tentatively Toxic

Sometimes we think we know everything about something only to find out we really don’t, said a Texas A&M University scientist.

Dr. Kevin Conway, assistant professor and curator of fishes with Texas A&M’s department of wildlife and fisheries sciences at College Station, has published a paper documenting a new species of clingfish and a startling new discovery in a second well-documented clingfish.

A venomous (right) and non-venomous (left) Caribbean clingfish showing the differences in the subopercular bone.

A venomous (right) and non-venomous (left) Caribbean clingfish showing the differences in the subopercular bone.

A venomous (right) and non-venomous (left) Caribbean clingfish showing the differences in the subopercular bone. (Texas A&M University photo courtesy Dr. Kevin Conway and Dr. Carole Baldwin, Smithsonian Institution)

The paper, entitled “Cryptic Diversity and Venom Glands in Western Atlantic Clingfishes of the Genus Acyrtus (Teleostei: Gobiesocidae),” was published May 13 in the PLOS ONE online journal. PLOS ONE is the Public Library of Science’s peer reviewed, open-access scientific journal.

The scientific paper documents the study Conway and his team, including Dr. Carole Baldwin, his collaborator at the Smithsonian Institution, and Macaulay White, former Texas A&M undergraduate, have been working on for several years.

“We are excited about the study, because it resulted in not only the discovery of an undescribed species, but also the discovery of a unique venom gland in a group of fishes nobody knew were venomous,” Conway said. “New groups of venomous fishes are not discovered very often, in fact the last such discovery happened back in the 1960s. The shocking thing is that the fishes that possess the venom gland have been known to science for a long time, some for over 260 years, and have been pretty well studied.”

Conway said he has not been involved in a discovery of this magnitude since he joined the Texas A&M faculty.

Conway said clingfishes are globally distributed at temperate and tropical latitudes, and get their name from their ability to anchor themselves using their large belly sucker. The species Conway and his team discovered is a tiny marine fish less than an inch long that lives between pieces of coral rubble in very shallow water along the coast of Belize and islands in the Caribbean and Bahamas.

Padded clingfish, Arcos nudus, a Caribbean clingfish with a subopercular venom gland described in the 1750s by Carolus Linnaeus

Padded clingfish, Arcos nudus, a Caribbean clingfish with a subopercular venom gland described in the 1750s by Carolus Linnaeus

“Our work shows that even in relatively well-studied areas of the world’s oceans, new species can be discovered as can unknown traits in well-documented species.” Conway said.

Conway explained that in order to describe a new species, taxonomists have to make comparisons with other closely related species to ensure they are not “rediscovering” something already  described by another researcher.

“During that comparison process we discovered that several species of Caribbean clingfishes, but not the new one we found, have a strange gland associated with a very sharp and spine-like subopercular bone, one of four bones that support the gill covers in fishes,” Conway said. “The cells inside the gland are incredibly similar to those present inside the venom glands of scorpion fishes and certain catfish and based on this similarity, we are confident that these clingfishes are also producing some type of toxin.”

“Discovering a venom gland in a group of well-studied fishes that has been known to science, some for well over two centuries, is truly remarkable,” Conway said.

Conway explained that most of the world’s 2,000-plus venomous species of  fishes deliver their venom using a modified fin ray, sharp opercular spine or even through a large fang in their lower jaw. But the venom gland they discovered in the Caribbean clingfishes associated with the subopercular gill cover bone is the first of its kind to be discovered and in fact, is unique among all venomous fish described to-date.

“We do not know exactly what the venom is used for, but based on the position of the venom gland, it is more likely that it would be used for protection, as in most venomous fishes.

“We don’t yet have any information about the toxic properties of these clingfishes, but we hope that our discovery will encourage other scientists to take a look at the venom gland we discovered in more detail,” he said.

Conway said clingfishes are referred to as crypto-benthic fishes which means “small, bottom dwellers.”

“Crypto-benthic fishes are not commercially important, but are considered by the scientific community to play an important role in marine ecosystems, because they are likely an important food resource for larger fishes,” Conway noted.

This article was originally posted in Texas A&M AgriLife Today.

You can support faculty research at Texas A&M University’s College of Agriculture and Life Sciences with a gift of an endowment to the Texas A&M Foundation.


Steve Blomstedt ’83
Senior Director of Development
(979) 845-9582

Howdy Farm Volunteers Honor the ‘Aggie’ Name

With every fruit, flower and leafy green bursting from the soil, Aggies are fulfilling the land-grant mission of Texas A&M University at Howdy Farm, a student-run sustainable farming project on West Campus providing the community with fresh produce and education about the merits of local agriculture.

“Not only does locally grown produce taste better, it’s healthier for people and the environment,” says John Adams, a senior ecological restoration and forestry major, and president of the Sustainable Agriculture Student Association (SASA) which operates Howdy Farm.


Senior John Adams, an ecological restoration and forestry major, and Taylor Paine, a horticulture graduate student, lead a team of student volunteers at Howdy Farm.

“We have bok choy, lettuce, peppers – we’re doing research trials for pepper varieties – every herb you can think of, tomatoes, flowering plants like hibiscus, sunflowers, potatoes, bananas. It’s a big mix of bright colors,” says Taylor Paine, a horticulture graduate student who serves as SASA’s market manager and treasurer.

Adams and Paine join a wealth of student volunteers who plant and maintain Howdy Farm and carry the produce to sell at local farmer’s markets.

“Local produce is picked when it’s ripe, versus what you get at the store,” says Paine. “Much of the produce you find at the store is picked too early, and can even be treated with ethylene gas to artificially ripen it.  When you buy food locally, it comes straight from the farm, it’s pesticide-free and fed with organic matter.”

Adams agrees, pointing to a 2014 study that found Texas is the worst state in the nation for access to locally grown food.

“Industrial agriculture has been very successful at producing crops,” he notes, “but it also has a massive impact on the environment. People are too willing to accept this notion that it’s a zero-sum game − that there is a necessary tradeoff between human needs and ecological integrity.

We have this ‘conquer, dominate, control’ mentality where it’s humans vs. nature,” he continues. “It’s time for a broad shift where we take an ecological world view, where we understand ourselves as parts of a larger system.”

Howdy Farm produces a wide variety of fruits and vegetables which are sold at local farmer's markets.

Howdy Farm produces a wide variety of fruits and vegetables which are sold at local farmer’s markets.

Allowing agriculture to follow ecological principles is key to health and sustainability, he adds, noting, “When we fight and degrade natural processes, we create problems for ourselves that we’re then constantly reacting to. For instance, under industrial practices, crops are grown in a way that makes them highly vulnerable to pests. So pesticides are used, which often creates a pesticide-resistant pest population while killing their natural predators and the crops’ natural pollinators.

We need to be taking a whole-system approach and when you do that, you’ll see there are synergies; it’s coherent − everything fits together.”

Besides the health and environmental benefits of local agriculture, Paine says farmers benefit greatly as well. “Farmers that grow food for mass consumption make 13 cents on the dollar,” she explains. “When food is grown and sold locally, the profit goes straight to the farmer because there is no middleman; it’s better for the local economy.”

Educating others about the benefits of sustainable farming is a key part of the Howdy Farm mission. The farm is used by Texas A&M Horticulture and other classes for experiential learning and for a variety of research projects.

And local schoolchildren are brought on field trips for tours of the farm by Aggies who instruct them on the methods and philosophies of local agriculture.

“I learned about how plants grow from seeds,” says second-grader, Sawyer H. “They gave my mom an okra seed and we’re going to plant it in our backyard.”

Adams says future plans for Howdy Farm include the construction of a building to be used as a center where members can gather for meetings, store educational materials and host guests.

He invites all Aggies and members of the community to volunteer at Howdy Farm. “Our volunteer hours are Mondays, Wednesdays and Fridays from 1-5 p.m. during the spring and fall semesters,” he says. “Just show up!”

This article was originally published by the TAMU Times.

You can support Texas A&M University’s Department of Student Affairs and the College of Agriculture and Life Sciences with a gift of an endowment to the Texas A&M Foundation.


Steve Blomstedt
Senior Director of Development
College of Agrilculture and Life Sciences
(979) 847-8655

How to Keep Fishing in the Amazon

Texas A&M scientists study what keeps freshwater fish abundant

On a recent plane trip to Santarem, Brazil, Kirk Winemiller gazed at a vast mosaic of lakes and waterways of the Amazon region. One huge muddy river split into multiple channels, each as wide as the Mississippi river.

The waters house over a thousand species of fish, which Winemiller, a professor in the Department of Wildlife and Fisheries Sciences, studies. The fish are an indispensable food resource and an essential part of the economy in this part of Brazil.

Dr. Leslie Winemiller (left) and Carol Arantes (right) process fish samples during a field survey of the river.

Dr. Leslie Winemiller (left) and Carol Arantes (right) process fish samples during a field survey of the river.

Each winter the rivers and lakes flood and water levels can rise by more than 30 feet, flooding forests and meadows. Researchers have known that fish migrate to flooded areas to feed on fruits, nuts, and seeds, but nobody has yet estimated how access to these resources influences fish production.

Amazon fish populations have decreased in recent decades, and the landscape has changed. Roughly 56 percent of the Amazon forest has been cut between 1970 and 2008.

To quantify the effect of deforestation on fish, Winemiller is working with a team of Texas A&M and Brazilian researchers. Leading the project is Winemiller’s doctoral student Carol Arantes. She is spending the 2013-2014 academic year examining fish specimens and conducting workshops with villagers on sustainable fishing. Once completed, the project will inform the work of government agencies and conservation groups in Brazil.

“The project is looking at the patterns of fish abundance in relation to vegetation in the floodplains, particularly whether or not there are more fish species and more fish biomass in areas where the forest is more intact,” Winemiller says.

“People in the Amazon depend so much on the fisheries,” he adds. “My lab conducts research on rivers in Texas, but we can also take our expertise to other countries to help people confronted with serious natural resource issues.”

Travel and living

Arantes has been renting a houseboat and hiring local fishermen to help catch and catalog fish. She stays at different locations for several days, collects environmental data, surveys fish stocks, processes fish samples, and preserves some samples for later study.

Winemiller and his wife, Leslie, traveled to Brazil during January and February to participate in the final field survey for the project.

Aerial view of the Amazon region near Santarem, Brazil.

Aerial view of the Amazon region near Santarem, Brazil.

“It’s a long day of travel,” Winemiller says. “We first arrived in the Manaus airport, right smack dab in the middle of the Amazon. One is surprised to learn that Manaus is a modern city of nearly 2 million people. From there we flew to Santarem where we headed out on the boat with Carol and her field team.”

They lived on a houseboat with 16 others, including the boat’s crew, local fishermen, student volunteers, and a cook. They slept in hammocks that swayed with the waves on windy, rainy nights.

“The cook was excellent,” Winemiller says. “The fish were delicious, and there were so many different kinds.”

Boating around the river afforded the team a close-up look at scattered villages and farms where people support themselves by fishing and raising livestock.

“There are seasonally flooded pastures that somehow support cows,” Winemiller says. “That was surprising to see along the shore of the Amazon River.”

When the river floods, big barges carry the livestock up and down the river to other pastures or to markets.

Houses in the floodplains are built on tall stilts. Despite the stilts, some houses are flooded with up to a foot of water during the rainy season. One woman said that she found a big lungfish swimming in her living room one year, Winemiller recounted.

Catching fish 

Arantes and Winemiller are comparing fish communities from regions that have been deforested with those where the forest remains intact, and they also will analyze the structure of fish communities during the different periods of the flood cycle.

By some counts, 1500 to 3000 species of fish can be found along the main channel of the Amazon. It would take years to survey all the species even in one location, Winemiller says. Arantes aims to focus her analyses on the fishes that are most common within each location.

“It would be a lot easier in a place like the Brazos River, where we only have maybe 40 fish species that are fairly common,” Winemiller says. “But we don’t need large samples. We try to get a few individuals of each species at each location during four different phases of the annual flood cycle.”

By April, Arantes had completed the last of four planned surveys. Now she needs to identify the remaining samples and bring fish samples back to be analyzed in the lab at Texas A&M.

In the lab, the preserved samples will be analyzed for stable isotopes: Ratios of carbon and nitrogen in fish tissues allow researchers to analyze the structure and dynamics of food webs, for example by determining whether a fish is a top predator or an herbivore.

Promoting conservation

The research Winemiller and Arantes are conducting will help Brazilian natural resource agencies and nongovernmental organizations in promoting conservation. Findings may help them promote the conservation of forests and the sustainable use of other natural resources, including fisheries.

Arantes is also conducting workshops to encourage community-based conservation. The strategies she teaches are aimed at allowing fish to survive long enough to grow and reproduce, which ultimately increases fishery yields. So far, at least two communities have embraced these strategies, and fish stocks are rebounding.

“They have monitored and limited their fishing effort and had a lot more fish and bigger fish,” Winemiller says. “That’s a preliminary finding without formal data analysis, but that’s encouraging. It means you really can manage more effectively. Hopefully this will convince people living on the Amazon floodplains to adopt better management practices.”

“I told you how huge the Amazon system is,” Winemiller says. “You wouldn’t believe that humans with small boats and nets could make an impact, but they really can.”

This story was originally published by the College of Agriculture and Life Sciences. 

You can support Texas A&M University’s College of Agriculture and Life Sciences with a gift of an endowment to the Texas A&M Foundation.


Steve Blomstedt ’83
Director of Development
College of Agriculture and Life Sciences
(979) 847-8655

Economics of using mesquite for electricity dependent on outside factors

Texas A&M research evaluates the pros and cons of harnessing mesquite for electricity

VERNON – Using mesquite biomass for electricity generation may become economically feasible if ecological and agricultural factors are considered, according to a Texas A&M AgriLife Research paper being published in the BioEnergy Research journal.


Mesquite biomass could be feasible for electricity generation if things like grass production were factored in.

“Economic Feasibility of Mesquite Biomass for Electricity Production: Projections of the Long-term Sustainability of Two Harvest Options” will appear in the April issue of the journal.

The paper was written by AgriLife Research personnel Dr. Jaesung Cho, postdoctoral associate; Dr. Seong Park, economist; Dr. Jim Ansley, rangeland ecologist; and Dr. Mustafa Mirik, associate research scientist, all in Vernon.

Their study estimated the long-term economic feasibility of mesquite biomass in electricity production under five different harvest scenarios, Park said. They examined variations in rates of standing biomass accumulation and tree density re-establishment after harvest using an above-ground-only or whole-plant harvest option.

Other work by Ansley has shown the heating value of mesquite is nearly equal to low grade coal.

The ecological and agricultural benefits of harvesting mesquite for bioenergy make it a potentially viable alternative to coal, Park said. More traditional income from these lands, such as livestock grazing and hunting, would be enhanced, and mesquite control costs would be reduced.

Current control methods of mesquite include herbicide sprays, mechanical treatments and prescribed fire, Ansley said. Herbicides and mechanical treatments can be costly for landowners. And prescribed fire, the least expensive option, has limited use due to the smoke distribution and higher risk of damage to non-target areas, especially during drought.

Increased grass production would lead directly to increased agricultural income through grazing by cattle, and leaving patches or strips of unharvested mesquite among harvested areas would increase wildlife habitat, he said. Mesquite reduction also could lower soil erosion due to the increased grass cover and increase off-site water yields into rivers and streams.

However, the researchers found some drawbacks to using mesquite as a bioenergy feedstock for electricity production. Re-growth and harvesting costs vary greatly, depending on the harvesting methods, rainfall and soil type. This can disrupt the supply of mesquite biomass for a power plant.

A previous study showed the re-establishment of mesquite biomass from emerging seedlings following whole-plant harvest would take considerably longer than regrowth from a plant with above-ground only harvest, Park said. The whole-plant harvest technique is considered to be less expensive compared to the above-ground harvest due to the difference in harvesting procedures.

However, the much greater re-establishment rate that occurs with the above-ground harvest options makes this more economically viable than the whole-plant harvest option, he said.

Mesquite also has a low applicability in existing power plants due to the high lignin content and its fibrous structure, Ansley said. Due to this structural limitation, mesquite biomass cannot be burned completely in the conventional firebox of existing power plants because coal mills cannot effectively produce a powder from the woody biomass.

The study determined pre-treatment techniques, such as torrefaction, which is a roasting of the wood to dry it down, and pelletization, may be required to increase the grindability, combustibility, uniformity, density, handling ability and energy efficiency of mesquite biomass during the electricity generation process, he said. This generates additional production costs.

Park said they concluded that, given the regrowth characteristic of mesquite and structural limitation of the biomass, a cost-effective processing method must be determined before recommending mesquite as a potential bioenergy feedstock.

Overall, he said, the study determined the above-ground harvest method, with 17 years of rotation length before re-harvest of the brushy regrowth, generated the largest economic returns to a power plant. It was more economically viable than a whole-plant harvest plan because of the much faster re-establishment rate before the next harvest. Frequency in the whole-plant harvest option could be as long as 40-50 years.

In addition, the above-ground harvest option was more viable because tree density would never decline – essentially all trees would re-establish shoots immediately after harvest – whereas, in the whole-plant option, the tree density level would have to be re-established from new seedlings, Ansley said.

“Regarding the economically optimum 17-year rotation for re-harvest in the above-ground scenario, this might be too long for ranchers interested in livestock grazing,” he said. “Typically, grass used for grazing will flourish for seven to eight years after mesquite is harvested, but at about 10 years, mesquite regrowth begins to out-compete grasses for water and light.”

So from a livestock production standpoint – and a selling point for ranchers to commit their pastures to periodic mesquite harvest in the above-ground scenario – harvesting every 10-12 years would be more attractive, he said.

Therefore, a biomass operation based on the above-ground harvest scenario may have to settle for a less-than-optimum harvest cycle to meet the needs of other income streams on a particular property, but would still be better in the long run economically than the whole-plant harvest option, Ansley said.

This article was originally published by Texas A&M AgriLife.

You can support Texas A&M University’s AgriLife and College of Agriculture & Life Sciences with a gift of an endowment to the Texas A&M Foundation.


Steve Blomstedt ’83

Director of Development
College of Agriculture and Life Sciences
(979) 847-8655


Smartphone app for livestock producers now available.

A smartphone app to help ranchers determine stocking rates is now available online. (Photo courtesy of AgriLife Extension)

A smartphone app to help ranchers determine stocking rates is now available online. (Photo courtesy of AgriLife Extension)

Livestock producers pondering stocking rates now have an app to help them determine that ratio, according to experts.

GrazingCalc is a new mobile smartphone application developed by personnel at Texas A&M University’s Department of Wildlife and Fisheries Sciences, and Ecosystem Science and Management units of the Texas A&M AgriLife Extension Service.

“One of the most common problems livestock managers deal with is determining the best number of livestock to have on the land without harming their resources,” said Blake Alldredge, an AgriLife Extension associate in College Station. “That task has just become easier with the release of this new app.”

GrazingCalc is now available for iPhone and other Apple devices at the iTunes Store at, Alldredge said.

“Being overstocked beyond what the land can handle may lead to overgrazing,” he said, “resulting in issues such as decreased forage production, erosion problems and degraded wildlife habitat,”

GrazingCalc is applicable anywhere because it is based on actual forage production as measured by the rancher, said Dr. Megan Clayton, an AgriLife Extension range specialist in Corpus Christi who, with Alldredge, developed the content of the app.

“Ranchers may need to do some work to obtain forage production on their property,” she said, “but it is easily done, and a video within the app demonstrates how to obtain this forage production value from their land.”

GrazingCalc allows ranchers to manipulate the number of types of animals, grazing months and remaining available forage.

Funding for the development of this app was provided through a Renewable Resources Extension Act grant from the Texas A&M Institute of Renewable Natural Resources.

This story was originally published in AgriLife Today.

You can support research in the College of Agriculture & Life Sciences at Texas A&M with the gift of an endowment to the Texas A&M Foundation. Request your A&M Support Kit to learn how you can help.


Steve Blomstedt ’83
Senior Director of Development
College of Agriculture and Life Sciences
(979) 847-8655

Saving Citrus

Residents can help save Texas' citrus industry.

Citrus does more than create jobs and pump money into the economy of the Lower Rio Grande Valley. It’s a way of life, a cultural staple dating back 100 years, part of the landscape and fabric of what makes extreme South Texas what it is, according to a plant disease expert. He’s now asking the people of the Valley to help keep the citrus industry from disappearing.

“We can see what’s happening to the citrus industry in Florida,” said Dr. Olufemi Alabi, a Texas A&M AgriLife Extension Service plant pathologist at the Texas A&M AgriLife Research and Extension Center at Weslaco. “The citrus industry in Florida is fast collapsing, due to a devastating disease called huanglongbing, or citrus greening. But here in South Texas, we can still fight this thing.”

The Rio Grande Valley’s citrus industry employs more than 1,000 people, earns growers $72 million annually, and has an economic impact of $134 million, according to Dr. Luis Ribera, an AgriLife Extension agricultural economist in Weslaco.

Citrus greening disease, which doesn’t harm humans but can wipe out entire orchards, has recently been found recently in a third area of the Valley, in La Blanca, a few miles east of Edinburg, on residential property. The bacterial disease has no cure yet, but Alabi believes that if everybody does their part, the Valley’s citrus industry can be saved.
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