Category Archives: International

Songbirds work around computational complexity by learning song vocabulary independently of sequence

song.JPG

(Dina Lipkind, Anja T. Zai, Alexander Hanuschkin, Gary F. Marcus, Ofer Tchernichovski & Richard H. Hahnloser 1 Nov 2017)

 

Songbirds, being skilled vocal learners18,19,20,21, provide an opportunity for studying how errors are assigned and minimized during the learning of complex motor sequences. A young zebra finch (Taeniopygia guttata) imitating an adult tutor has to match a series of spectrally distinct sounds (syllables) performed in a precise order (Fig. 1b). Zebra finches are capable of adjusting their developing song towards its target in a variety of ways, including morphing the spectral (phonological) structure of song syllables22,23,24,25, generating and adding novel syllables to their song23, 25, 26, and rearranging the positions of existing syllables26, 27. How then do they cope with the complexity of selecting the appropriate combination of operations that would reduce the mismatch between their own song and the target?

A possible way to reduce computational complexity could be to optimize one aspect of the task, while ignoring the costs of the other. At one extreme, the task could be reduced to assigning each syllable in the bird’s song to the temporally corresponding syllable in the target song (Fig. 1c, left). Such strategy would minimize sequence rearrangements, at the cost of possibly large phonological adjustments. Although this hypothesis has not been directly tested, a number of previous findings suggest that songbirds may not be using global alignment between song and target as a learning strategy. These include the observation that individual syllables are recognizable in developing zebra finch song before the correct sequence is apparent28; the existence of an early developmental phase in which repetitions of a single “proto-syllable” differentiate towards multiple targets22, 24, 25, 29, 30; the fact that many songbird species perform variable syllable sequences as adults (e.g., nightingales, starlings and Bengalese finches); and the ability of zebra finches to match a target exclusively through syllable rearrangements, without changing phonology26. An alternative strategy, therefore, could be to assign song syllables to target syllables in a manner that minimizes phonological distances, while ignoring combinatorial distances (Fig. 1c, middle). Such phonological greediness would increase the number of ensuing sequence changes and thus the overall sequencing cost26. An intermediate strategy could be to seek a trade-off between minimizing structural and temporal errors, for example by independently matching parts of the song sequence (such as phonology in bigrams or trigrams27) to parts of the target sequence

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A warbler’s flashy yellow throat? There are genes for that

warbler2.JPG

(University of British Columbia. 8 Oct 2017; Photo Alan Brelsford)

Birds get their bright red, orange and yellow plumage from carotenoid pigments—responsible for many of the same bright colours in plants. But how songbirds turn carotenoids into the spectacular variety of feathered patches found in nature has remained a mystery.

Now University of British Columbia (UBC) research might have pinpointed some of the genetic machinery responsible for the plumage colouration in Audubon’s and myrtle warblers, related but distinctly feathered North American songbirds.

“Audubon’s and myrtle warblers interbreed in a narrow band across British Columbia and Alberta,” says David Toews, co-author of a new Proceedings of the Royal Society paper exploring the birds’ colouration.

“Those hybrid warblers, while considered oddities to some birders, were key for this study because their plumage traits and genes are all jumbled and mixed, allowing us to link their differing colours to genetic markers and hopefully the genes responsible.”

Both types of warblers use colourful carotenoid pigments to make several yellow feather patches, including their yellow-rumps—the birds are colloquially referred to as ‘butter butts’.

But only Audubon’s also used carotenoids in their telltale yellow throats. Myrtles have white throats and the hybrids have a mix of white and yellow.

The study identified several genomic region s— one including a member of the scavenger receptor gene family that affects carotenoids in other animals—that might be involved in this selective distribution of yellow carotenoid colours.

“We found strong associations with several genomic regions across a handful of distinct plumage traits” explains co-author Alan Brelsford. “Now we can now dig even deeper into these regions to understand the mechanisms that make warblers so colourful and diverse.”

“This study is unusual in that it focused on variation in multiple colour patterning traits,” says co-author Darren Irwin, a professor of zoology at UBC. “Two of the plumage differences between the species, eye spot and eye line colouration, appear to be encoded by a single region in the genome.”

How Wildfires Affect Birds

(By Andy McGlashen, 11 Oct 2017; Photo:Robert Royse)

Big burns are natural, but climate change could make especially destructive fire seasons the new normal.

Devastating and deadly wildfires in California’s wine country this week made it clear that this summer’s brutal fire season in the West isn’t over yet. Nationwide, 38 fires are still burning, 17 of them large and uncontained, according to a daily report from the National Interagency Fire Center. Fires have scorched more than 8.5 million acres in 2017 so far, compared to a 10-year average of about 6 million acres. Multiple firefighters and citizens have died in blazes this season, and thousands of homes and businesses have been destroyed. Smoke has made the air dangerous to breathe in many parts of the West.

Like melting glaciers and rising seas, larger fires and longer fire seasons are among the predicted effects of climate change that are now coming to pass. With that in mind, it’s worth exploring how wildfires affect birds. It’s hard to definitively say how avian communities will be affected in the long term, but generally speaking—for now, anyway—wildfires don’t pose a major threat for most birds.

What do birds do when wildfires break out? No surprise here: They fly away. A fire might kill weak birds or, depending on the time of year, claim nestlings. But at least in the Western forests that U.S. Forest Service research biologist Vicki Saab studies, birds evolved alongside fire and flee in the face of conflagrations. “Direct mortality is not a big concern,” Saab says.

How do wildfires physically affect birds? Assuming birds escape a fire, smoke might still affect their health in ways that aren’t very well understood. “We do know that exposure to particulate matter, which of course is of great concern for human health, can affect birds as well,” says Olivia Sanderfoot, a National Science Foundation Graduate Research Fellow at the University of Washington Seattle who studies how air pollution affects birds. For example, veterinarians and poultry scientists who study captive birds have found that smoke can damage lung tissue and leave the animals susceptible to potentially lethal respiratory infections.

How that plays out in the wild is largely unknown, Sanderfoot says. Her current research aims to track changes in bird populations and diversity after exposure to smoke from large wildfires. In some cases, smoke inhalation might make it harder for birds to flee onrushing flames. Thick smoke, for instance, may have contributed to the deaths of 50 adult White Ibises during a 1999 fire in the Everglades, Sanderfoot reported in a recent paper. And some low-flying species might succumb to smoke inhalation or exhaustion before they can escape forest fires, according to the Alberta Institute for Wildlife Conservation.

How do wildfires affect habitat, and do any birds benefit from blazes? A little disturbance is a good thing for many species. In the dry, mixed-conifer forests Saab studies, most wildfires—even intense ones—burn unevenly, leaving behind a mosaic of habitat patches. “Fire definitely benefits a lot of bird species,” Saab says. “It’s not all doom and gloom.”

For a Black-backed Woodpecker, for example, a newly burned forest provides a smorgasbord. Bark- and wood-boring beetles arrive in droves and lay eggs in charred trees; woodpeckers feast when they reach the larval stage. There’s often an influx of other bugs, too, which draws aerial insectivores like Dusky Flycatchers and Mountain Bluebirds that hunt for midair meals in the new forest openings created by fire, Saab says. The patchwork of post-fire habitats also suits White-headed Woodpeckers and other species that nest in open areas but forage in unburned surrounding forests.

Other birds benefit from fires over the longer term. Kirtland’s Warbler, for instance, nests only in the fire-dependent jack pine forests of Michigan, Wisconsin, and Ontario. Jack pine cones are sealed tight with resin until fire opens them up, releasing the seeds and generating new warbler habitat. Red-headed Woodpeckers, which nest in the high limbs of dead trees, can see a local population boom after a fire devastates a patch of forest.

Blazes aren’t a boon for all avian species. Wildfire forces those that dwell in old-growth forests—including Pileated Woodpeckers, Townsend’s Warblers, and Golden-crowned Kinglets—to go in search of new places to nest and forage. It also poses a serious risk to a bird that faces plenty of other threats: the Greater Sage-Grouse. Fire in the sagebrush ecosystem—upon which this iconic species depends—often gives invasive plants such as cheatgrass and juniper a leg up on slower-growing sage, and they provide fuel for future fires.

Do birds ever start wildfires? When combined with electricity, yes. We’ve all seen birds perched harmlessly on power lines. But if they manage to touch two transmission lines at once, they form a circuit and get zapped. In two recent fires started by birds, hawks were carrying snakes. Chances are, those writhing meals-to-be touched the second power line, electrocuting dinner and diner both, and sparking the blaze below.

There are credible claims that birds intentionally spread fires, too. Audubon and other publications have covered anecdotal reports of northern Australia raptors picking up burning sticks and dropping them elsewhere on the arid landscape to flush out prey like lizards and snakes. Mark Bonta, the Penn State geographer behind those reports, says that he and colleagues have a forthcoming peer-reviewed paper with further evidence that Black Kites, Brown Falcons, and Whistling Kites all spread fires intentionally. The researchers haven’t yet captured video or photographic evidence of the phenomenon, but Bonta says they’ve confirmed it by interviewing local experts and reviewing publications of aboriginal knowledge.

How big of a role does climate change play? Researchers detect a changing climate’s fingerprints on this year’s ferocious fires, which may be just a glimpse of things to come. In northern California, for example, heavy winter rains fueled a riot of new plant growth in the spring, but the summer’s record heat parched that vegetation, turning it to tinder. That’s part of a broader trend; Columbia University scientists last year showed that climate change has doubled the area of the western U.S. affected by forest fires over the past three decades. “Climate is really running the show in terms of what burns,” one of that study’s authors said. “We should be getting ready for bigger fire years than those familiar to previous generations.”

What climate-charged fires will mean for birds is hard to say. “More and more, the past is becoming irrelevant as we advance to the no-analog future climate,” one researcher told Audubon in 2015. Saab, from the Forest Service, says she expects future fires to rearrange habitat types and the distribution of bird species. For now, the patchwork of habitat left behind by blazes helps maintain bird diversity in Western forests. “In the future?” she says, “I don’t know.”

Cover crops provide bed and breakfast layover for migrating birds

(University of Illinois, 30 Oct 2017;Photo Cassandra Wilcoxen)

After harvesting a corn or soybean crop, farmers may plant a cover crop for a variety of reasons — to reduce soil erosion and nutrient runoff, increase organic matter in the soil, and improve water quality. Now there’s another reason. University of Illinois research shows that migratory birds prefer to rest and refuel in fields with cover crops.

“Here in the Midwest, we’re in one of the major flyway zones for migratory birds, where there once was plenty of habitat for grassland birds to safely forage and rest during their migration. Now that agriculture is the dominant landscape, they’re finding it harder to get the resources they need on the way to their breeding grounds,” says Cassandra Wilcoxen, a graduate research assistant in the Department of Natural Resources and Environmental Sciences in the College of Agricultural, Consumer and Environmental Sciences at U of I.

“We think cover crops, such as cereal rye, likely provide migrating birds with more vegetation and a safe area to escape from the elements and from predators,” Wilcoxen says. “Cover crops also increase insect abundance, another food source for birds. The increased number of insects allows migrants to fuel up faster and move on to their breeding grounds.

“Grassland birds prefer large, open areas: the bigger, the better. Agricultural fields are huge, so the cover crops provide a large habitat where birds can rest, forage, and potentially even nest.”

Fields with cover crops are not going to replace natural habitats, but in early spring there can be miles of fields with little vegetation. The advent of cover crops provides a potentially important habitat for birds returning to the Midwest from areas as far south as Argentina. The large green fields are likely a beacon for migratory birds.

Over two planting seasons, Wilcoxen monitored birds in corn and soybean fields with and without cover crops. She observed 6,133 individual birds of 52 species, with 13 species accounting for 90 percent of all birds detected. The most common species were the red-winged blackbird, common grackle, and American robin.

“Fields with cover crops always had more birds, and corn fields with a cover crop were the overall winners,” Wilcoxen says. She thinks corn plus a cover crop, especially cereal rye, was the favorite because there is more residue on the fields; the remaining corn stalks along with rye provide more cover for the birds.

What’s the downside? Wilcoxen says it’s all in the timing.

“The window of time to plant a cover crop in the fall is fairly short. Cover crops can be aerial seeded, drilled, or broadcast. But depending on how wet the fall is, there is only a short time when it can be planted. Drilling is the best method because you know you’re getting good seed-to-soil contact,” she says.

Another timing issue emerges in the spring: when to kill the cover crop.

Wilcoxen says it’s tricky. “Some grassland birds nest in the spring, so in order to give birds the time they need, farmers may need to hold off terminating their cover crop. Those are the sorts of recommendations that will require more research,” she says. “It’s true of any new farming practice. You have to play around with it to get it right.”

“In our experience, most farmers using cover crops have learned about the practice from their neighbors, and we are hoping this continues and cover crop use continues to grow,” Wilcoxen says.

Will what’s best for migratory birds motivate farmers to plant cover crops and terminate them a bit later to allow birds to use them for habitat? Wilcoxen is hopeful. She says one of the aspects of her work that she enjoys most is bringing together the agricultural community and the wildlife community to work together for long-term environmental health.

“Production agriculture has taken a lot of habitat from wildlife, but we need it to provide food for us and the world. But how do we mesh the two? Where are the opportunities? No-till is a great example. It helps slow soil erosion and it helps birds. Now cover crops are another overlapping win-win opportunity to benefit both agriculture and wildlife.”

Native trees, shrubs provide more food for birds

(University of Delaware 31 Oct 2017; Photo;Desiree Narango and Doug Tallamy)

University of Delaware doctoral student Desiree Narango is researching trees and shrubs planted in the lawns of homeowners throughout the Washington, D.C., Maryland and northern Virginia areas to assess how those choices are impacting food webs.

Narango, who is working with Doug Tallamy, professor of entomology in UD’s Department of Entomology and Wildlife Ecology, is also associated with the Smithsonian Migratory Bird Center and works through a citizen-science program called “Neighborhood Nest Watch.” Narango is co-advised by Pete Marra, director of the Smithsonian Migratory Bird Center.

Through her research, Narango looks at breeding birds and the food resources they need, such as insects and caterpillars.

Different trees vary in how much food they provide birds, and Narango said she has a network of homeowners in the D.C. metropolitan area who allowed her to use their yards for her study. Over the course of the four-year study, Narango has looked at 203 yards.

One thing that has stood out to her is the sheer number of different trees that are planted in these yards.

“We focus on woody plants — so trees and shrubs — and we’ve documented over 375 different species in these 203 yards. Which is crazy,” said Narango who added that it became apparent quickly that some trees are better than others with regard to sustaining food webs.

“We just had a paper come out in the journal of Biological Conservation where we show that native trees are better at providing caterpillars for birds, which is a really important food resource,” said Narango. “Native trees are better, hands down, but even among the native trees, there are some that are better than others so things like oaks and cherries and elms are highly productive for caterpillars, so they have lots of good food for the birds.”

Narango added that there are a lot of non-native plants — such as zelkova, ginkgo and lilac — that don’t provide any resources for breeding birds.

“Those species are true non-natives so they’re not related to anything here, and they provide almost nothing in terms of caterpillars for birds,” said Narango. “There are also species like Japanese cherry and Japanese maple that are non-native but are related to our native maples and cherries. We found that those species have an average of 40 percent fewer caterpillars than the native versions of that tree. If you had a choice between a black cherry and a Japanese cherry and if you’re interested in food for birds, then you should choose the native version.”

Narango said that a problem homeowners may face when trying to select native versions of plants is that a lot of the big box stores don’t carry them.

“There are a lot of really great small nurseries that have many native plants that are productive in terms of caterpillars and are also very beautiful,” said Narango. “You definitely don’t have to sacrifice beauty to get plants that are ecologically beneficial. There’s a lot to choose from so you can have beauty, you can have fruit and then also have food for birds, too. It’s all interconnected.”

As for the most eye-opening aspect of her research, Narango said that it has to be the tremendous amount of diversity in bugs and birds in people’s backyards.

“A lot of people think you need to go to the woods to see beautiful butterflies or beautiful birds, but they’re actually in people’s backyards, too,” said Narango.

In the group’s bird surveys, they documented 98 different bird species.

Narango focuses on the Carolina chickadee and said that she would follow individual birds around to see what trees they were choosing. One of the major findings in her paper is that the number of caterpillar species a plant supports predicts how strongly chickadees prefer it.

“When these birds would choose a tree, all the other birds in the neighborhood were choosing those trees, too. So we would see these amazing warblers that don’t breed in Delaware or in D.C. but are migrating through, and they’re using all these suburban habitats on their way north. In a way, our chickadees were telling us what all of the birds want during that period,” said Narango.

As a landscaper herself, Narango added that it was surprising to see how much life happened in her own backyard when she started planting the right species.

“I planted this flower called ironweed, and the first year it was there, I had the specialist bees that use that flower and then I have caterpillars in my shrubs, and it’s really cool how quickly you can see life be attracted to your yard when you plant the right species,” she said.

Penguins’ Calls Are Influenced by Their Habitat

AUK-17-75 D Colombelli-Negrel

(AOS 1 nov 2017;Photo: D. Colombelli-Négrel)

Birds use vocalizations to attract mates, defend territories, and recognize fellow members of their species. But while we know a lot about how variations in vocalizations play out between populations of songbirds, it’s far less clear how this variation affects birds such as penguins in which calls are inherited. A new study from The Auk: Ornithological Advances examines differences in the calls of Little Penguins from four colonies in Australia—nocturnal birds for whom vocalizations are more important that visual signals—and finds that disparities in habitat, rather than geographic isolation or other factors, seem to be the key driver of variation in the sounds these birds use to communicate.

Diane Colombelli-Négrel and Rachel Smale of Australia’s Flinders University recorded calls from four Little Penguin populations across a small area of South Australia, one of which had previously been shown to have subtle genetic differences from the other three, and used playback experiments to test penguins’ ability to distinguish between calls from different colonies. They found that agonistic calls, which are used in pair displays and aggressive situations, varied among the four populations, and that the calls’ characteristics appeared to depend on small-scale differences in the habitat where the penguins lived. However, birds did not discriminate between calls originating from different colonies, which suggests that agonistic calls don’t seem to play a role in isolating the two different genetic groups.

Penguins breeding in open habitats produced lower-frequency calls than those breeding in habitats with denser vegetation—the opposite of the trend typically observed in songbirds. The authors speculate that agonistic calls may be subject to different selective pressures because they’re used in close encounters with other birds rather than to communicate across distances, and could also be influenced by variation in the noise level of wind and surf. “I was excited to find that calls were influenced by habitat, as this hasn’t been investigated much in seabirds and most of our knowledge in this area comes from studies on songbirds,” says Colombelli-Négrel. “This new research suggests that many factors influence call variation in birds, which also depends on the function of the calls. This study highlights that many questions remain and that studies need to investigate more than one factor in conjunction with the function of the calls to fully understand call variation in seabirds.”

“This work tells an interesting story of vocal diversification in Little Penguins, and gives insight into how individual and micro-scale variation effects behavior,” according to Stony Brook University’s Heather Lynch, an expert on penguin calls who was not involved in the study. “Non-vocal-learning birds are relatively understudied in terms of vocalizations, and it is great to see penguin vocalizations being studied in such a way.”

How songbirds learn a new song

ETH Zurich, ScienceDaily; Photo1nov 2017

For a songbird, learning a new song is akin to a child learning a new language. Zebra finches approach this challenge step by step, and even make a detour in the process — by taking song syllables that they already know and adapting them to the syllables that they have to learn. During this learning phase, the syllable sequence often gets mixed up. The birds then arrange the newly-learned syllables into the correct order in the next learning phase. Researchers led by Richard Hahnloser, a professor at the Institute of Neuroinformatics run by ETH Zurich and the University of Zurich, have reported these findings in the latest edition of the journal Nature Communications.

“The zebra finches have evolved the strategy of dividing a task as complex as learning a new song into easy-to-manage parts,” says Hahnloser. “This allows them to expand their repertoire with minimal effort.”

The scientists made this discovery in an experiment with young birds that were less than a month old at the start of the study. On a daily basis, the researchers broadcasted a song to the birds, which the birds then learned. After a month, the researchers changed the song and the birds tried to adapt their song to the new one. “In nature, birds instinctively adapt their songs to those of adult birds of the same species,” explains Hahnloser. The researchers recorded all vocalizations made by the birds and used a computer to evaluate them syllable by syllable.

Sound examples

The letters represent different syllables (each of a specific pitch): + and — for a positive and negative semitone change, ++ for a whole tone change.

Bird that has mastered song ABC, with the task of learning song AC++B. In a first step, the bird changes the pitch of syllable C and sings ABC++. Only in a second step does the bird arrange the syllables in the correct order AC++B.

Bird that learned the song ABCB+ in the first place, with the difficult task of learning a second song AB++CB-. The bird must learn to sing syllable B both a whole tone higher and a whole tone lower. To do this, it makes a detour via the song AB-CB++. This means that it first changes the syllables each by a semitone (two small changes) and then tries to arrange the syllables into the correct order — which actually not a single bird achieved in the experiment. The birds reached adulthood during the course of the experiment; adult birds no longer change their song.

Computer linguistics with similar methods

“Interestingly, the birds’ strategy closely resembles the best methods currently used in computer linguistics to compare documents,” says Hahnloser. These algorithms compare written documents by considering their words in their context but regardless of their exact order. By comparing billions of texts, these algorithms can estimate the similarity of two words in terms of a number. In this way, for example, they identify that the words “house” and “building” have almost the same meaning.

These computer programs can also search through millions of documents to identify which is most similar to a given text, by determining which document contains the vocabulary that can be most easily adapted into the vocabulary of the comparison text. “Today’s computer scientists therefore use the same strategy that songbirds evolved — the birds have probably been using it for millions of years,” says Hahnloser.

Hypotheses for studies on humans

It is still uncertain whether infants use a similar approach when they learn their first or second language. However, Hahnloser believes that there are numerous similarities between the way humans learn to speak and the way birds learn their songs. Songbird research has already shown striking parallels with speech development in young children. For example, earlier studies showed that young birds and young children practise every single syllable extensively through duplication (with children, for example, “baba” or “dodo”). These studies showed that both continue to do so when learning new syllables even after they already mastered vocalizations containing two different syllables (with children, for example, “rabbit”).

Hahnloser’s latest research into songbirds has led to the hypothesis that young children also use a minimalist approach when it comes to learning a foreign language; they learn new sounds (for example, the nasal vowels or rolling of the R in French) by minimally adapting the sounds they already know, at first without considering the context of these sounds in the foreign language. However, further studies are still required to ascertain whether this is in fact the case.