Barcode turns 40

Today is a very special day for a technology that has become the eponym for most DNA-based identifications. Reason enough to devote a blog post on its birthday:

On June 26th, 1974, a 10-pack of Juicy Fruit Gum was scanned for its Universal Product Code (UPC) at a food store in Troy, Ohio.

Forty years later, the barcode is printed or embedded on trillions of products and other things worldwide. Furthermore, it is available in dozens of modern formats.

The number of applications of barcodes is actually growing faster than ever. In the past five years, it's been given a boost by the emergence of smartphones equipped with digital cameras that - with the right app - can be used as barcode scanners. More recently, faster processors have arrived that can read thousands of alphanumeric characters on a single imprint, which can be smaller than a postage stamp.

In the past eight years, barcodes have become so varied and complex that optical imagers can read QR codes or matrix barcodes to learn not only the identity and price of a product but also very specific information including the serial number of a precise product. It is now possible to track down a particular machine part's identification to learn through a connected database when, where and how it was created or who inspected it - all of which can prove essential in accident investigations or recalls.

Today barcodes are so commonplace that we take them for granted. We load a boarding pass barcode onto a smartphone display that's read at the gate. Everything we buy is scanned at the cashier and the technology enabled big stores to install self-serve cash registers where customers scan their own groceries. Nurses check in patients and re-check them several times for surgical procedures or other treatments by scanning barcodes on their wrists that are compared to barcodes on their charts. Pharmacists track medicines, while warehouse workers and courier drivers use handheld scanners to track goods and packages at lightning speed. A utility worker scans a meter connected to a customer's history, while a mechanic can research a car part's history and so on.

IBM engineer George Laurer, invented what became the UPC barcode first used on that pack of gum in 1974. However it took quite some time and various standards groups involving members from multiple companies and governments to get the movement started and then to later review a steady stream of alterations and innovations.

The roots of barcodes go back much further. A U.S. patent was granted in 1934 for a card sorter device that was able to read a simple code consisting of four bars printed on paper. The printed bars were read by photoelectric cells. The goal was to automate the payment of utility bills, with the primitive four bar barcode printed on a postcard sent to each customer then later read when the payment was made.

The development of the barcode was a revolution. There is nothing I can think of that had a greater impact on facilitating commerce around the world than the UPC barcode. Happy birthday!

A not so cute ladybird

Yesterday I wrote about biocontrol agents to manage aphid infestations. One species that was introduced from Asia to North and South America, Europe and Africa, for use in biological control programs is the harlequin ladybird Harmonia axyridis. Since its introduction in 1988 it has established populations in at least 38 countries and spreads at a rate of approximately 200 km/yr.

The harlequin ladybird is a large, voracious and resilient coccinellid beetle and has a long history of use as a classical biological control agent of aphids and scale insects since 1916. It is a highly polymorphic species (see image), with variation in colour morphs evident across its range, and has thus long been a study species for geneticists. Unfortunately, this species has itself become a pest. For example in the autumn, these beetles can aggregate in large numbers in vineyards and, if they are harvested along with the grapes, they release a chemical compound called methoxypyrazine that can spoil the aroma and taste of the wine. This species is also known to invade homes in October in preparation for winter, a phenomenon which earned it the common name of “Halloween lady beetle”. They try to overwinter indoors and there also have been reports that they occasionally bite humans.

However, the worst impact stems from a phenomenon called intraguild predation (IGP), i.e. the killing and eating of a species that uses similar, often limiting, resources. Here the targets are native species populations that are attached by Harmonia axyridis. 

A new study published by a group of researchers from the UK, Belgium and the Netherlands is the first to use DNA Barcoding to identify prey species in the guts of harlequin ladybirds showing their damaging effect on native species. Their results strengthen the evidence that Harmonia axyridis is a very generalist predator. The researchers used barcodes to screen for four possible intraguild prey species (the two ladybirds Adalia bipunctata and Adalia decempunctata, as well as the hover fly Episyrphus balteatus and the lacewing Chrysoperla carnea) is occurring in the wild. Three of the four target prey species were detected in the guts of  guts of 177 larvae field-collected in England, France, Germany, Slovakia and the Czech Republic: Adalia decempunctata, Adalia bipunctata and Episyrphus balteatus. The lacewing Chrysoperla carnea was not detected. Nevertheless, the results suggest that Harmonia axyridis feeding on alternative prey in the wild is commonplace and that can have negative effects on native species across a wide geographic area.

I am not sure if Harmonia the ancient Greek goddess of harmony likes her ever hungry namesake.

Barcoding potential biocontrol agents

The soybean aphid (Aphis glycines) is an insect pest of soybean (Glycine max). The soybean aphid is native to Asia.but has been introduced to North America in 2000.  It has also been described as a common pest of soybeans in China and as an occasional pest of soybeans in South East Asia.

Soybean aphids suck fluids from soybean plants. The most important effect of aphid damage on yield is the reduction in the number of soybean pods. Thus, yield may be affected most when soybean aphids attack soybean plants that are flowering or setting pods. Sooty mold typically appears on heavily infested plants. The soybean aphid is also capable of transmitting several viruses that infect soybean, such as soybean dwarf virus and soybean mosaic virus.

Soybean aphid have a complex life cycle with as many as 18 generations annually. Two different host plants are required by the aphid. It spends the winter on buckthorn plants (Rhamnus) as eggs. Nymphs hatch in the spring, and after a few generations on buckthorn, winged females fly in search of soybean plants. The aphids pass through a series of wingless and winged generations on soybean during the summer. In September, winged aphids migrate to buckthorn plants to complete their annual life cycle.

In Asia, the soybean aphid experiences pressure from over 30 species of predators, 8 species of parasitoids, and some fungal pathogens. Field studies in showed that particularly some species of hymenopteran parasitoids contribute a lot to the drastic reduction of soybean aphid populations, e.g. Lysiphlebia japonica was determined as a keystone aphid parasitoid in the ecosystems and agro-ecosystems of Korea and China with parasitism rates of over 50%. This makes them ideal candidates for biocontrol agents that could be used to fight the aphids without extensive use of insecticides. 

However, the correct identification of these parasitoids is crucial for assessing their potential in biological control projects. Misidentification may result in serious economic losses. Due to their small body size (usually 0.5–2.0 mm), high-quality slide and card-mounted specimens are needed in traditional morphological identification. Even well-known species can be confused with closely related sister species.

That is the reason why a group of Chinese researchers tested the utility of DNA Barcoding to assist with parasitoid identification which to no surprise worked quite well:

The DNA barcoding approach greatly assisted the identification of the parasitoid complex of the soybean aphid in China. Our results revealed 15 species belonging to 10 genera of five Hymenoptera families. The DNA barcodes show high interspecific distance coupled with low intraspecific distance. 

It seems that DNA Barcoding not only allows us to identify pest species but also parasitoids we can use to fit them:

A reliable and comprehensive DNA database of insect pests and parasitoids is required for rapid species identification and understanding the parasitoid community. Accurate identification using DNA barcoding could be a pivotal step in the assessment of their performance and suitability as biocontrol agents in biological control programs

Busting an invasion myth

According to experts there are more than 12,000 non-native species in Europe, and the number is increasing. Introduced species are one of the main threats to biodiversity and are causing immense economic damage, however, not all introduced species are actually problematic. In April 2014 the EU parliament approved EU-wide measures to ban further import of non-native species and to improve the management of already established invasive species.

Spanish slugs (Arion lusitanicus) are one of the most common slug species in Central Europe. For some time conservationists have observed that the rapidly growing number of Spanish slugs is replacing the native black slug in Central Europe as well as inflicting significant damage on natural vegetation and agricultural products. Today Arion lusitanicus is the most common species of snail in Germany. It is also ranked among the "100 of the worst" invasive animal and plant species in Central Europe that are thought to have a significant negative impact on biodiversity, economy and health. The animals are sometimes nicknamed “killer slugs” because of the damage the cause in fields and gardens. Allegedly the Spanish Slug made its way to Central Europe with imports of fruit and vegetables in the 1950s.

However, researchers of the German Biodiversity and Climate Centre and the Goethe University in Frankfurt now found out, that the prime example of an invasive species is originally from Central Europe and thus no "immigrant" after all. Control measures, such as the EU regulation on prevention, early warning, rapid response, and management of invasive species which is being discussed currently, would therefore not apply to this species.

They used statistical phylogeographic techniques on the barcode region (COI) and a nuclear (nuclear zinc finger-like locus ZF) marker as well as species distribution modelling to show that the species is with very high probability not an invader, but native to Central Europe. The group led by my former Masters supervisor Markus Pfenninger also found several cryptic species in what was supposed to by one species:

Our DNA-taxonomy approach indicated the dire need of a thorough integrative taxonomic revision of the entire genus Arion. The presence of many unnamed, mostly highly divergent haplotype clades calls for thorough integrative taxonomic studies on their specific status, as several previous studies in Arion have revealed the presence of undescribed species.

Slugs already have a poor reputation because of their sliminess and their immense appetite for the veggies we cultivate. That is already unfair. They are fascinating creatures and don't deserve to be detested. At least the Spanish slug  is now cleared from the allegation of being invasive. That is a step forward.

Climate change deflecting attention from biodiversity loss

Recent high levels of media coverage for climate change may have deflected attention and funding from biodiversity loss, colleagues from the Kent Durrell Institute of Conservation and Ecology suggest. In a new paper they recommend that, to prevent biodiversity from becoming a declining priority, conservationists need to leverage the importance of climate change to obtain more funds and draw attention to other research areas such as biodiversity conservation.

For the study, the team conducted a content analysis of newspaper coverage in four US broadsheets (The New York Times, The Washington Post, The Wall Street Journal, and USA Today) and four UK broadsheets (the Guardian, The Independent, The Times, and the Financial Times). Academic peer-reviewed coverage and project funding by the World Bank and National Science Foundation were also examined.

Among their findings they discovered that:

• Press attention devoted to biodiversity has remained stable since 1990, but the proportion of climate change reports rose before 2007 and has stayed substantially higher than biodiversity since 2005.
• In scientific journals, papers on biodiversity loss and conservation have increased at a steady pace, but publication of papers on climate change accelerated markedly around 2006 and overtook them
• Funding by the World Bank shows no evident change over the past 20 years, with climate change projects funded at a much greater rate than biodiversity projects. The US National Science Foundation's investments directed toward climate change research have increased substantially since 1987, but biodiversity expenditures have increased much less and have held steady since 2004.

The researchers recommend that, given that many human influences are driving both climate change and biodiversity loss, conservationists should aim for win-win solutions such as the United Nations program REDD+ (an extension of the Reducing Emissions from Deforestation and forest Degradation program).

The objective of REDD+ is not just to secure carbon storage but also to create additional cobenefits for local communities and biodiversity. Such mechanisms avoid the artificial prioritization of one particular environmental threat over another, providing unifying approaches that can be promoted to different stakeholders 

From the inbox

Just received this via email: Bees and honey, bats, and...tequila? Happy National Pollinator Week! The Museum’s scientists have been busy recounting stories about the intricate relationships between plants and their pollinators. Tomorrow at 1pm ET, @NMNH will host a live Twitter chat moderated by Dr. Gary Krupnick, head of the Museum’s Plant Conservation Unit. He’ll be joined by experts from the U.S. Geological Survey and the Pollinator Partnership. We would like to hear from you! Send your questions using the hashtag #SIpollinator. P.S. Want a quick refresher on pollination? Head to the Q?rius website. Masthead photo: Bumble bee (Bombus sp.) taken at the NMNH Butterfly Habitat Garden. Credit: Rosa Pineda, Smithsonian Institution

School Malaise Trap Program Spring 2014

It's time again to share some results of a School Malaise Trap program. The spring program ran from April 22nd to May 5th involved 54 schools in 41 cities, 93 classrooms, and 2,258 students. All participating teachers will receive an email today with a big results package.

As a result of a rather long winter we had relatively cool spring temperatures during the trap deployment period. Consequently we were expecting less species and specimens than during the same period last year.

Indeed the trap catches were lower. The 58 traps on average collected 482 specimens for the collecting period. Our staff sorted 27,965 specimens and selected 12,968 to be barcoded. Our final dataset was made up of 11,425 DNA Barcodes (not all worked and short barcodes were discarded). A still impressive number of 704 putative species were collected over the two week period of the program. Here the taxonomic breakdown:

20 of these species were new to BOLD which could either mean that they are known but have not been sampled yet or that they are indeed new to the region or even to science. Last spring, 60 schools participated in the School Malaise Trap Program and collectively they were able to find some 1,400 species and almost 100,000 individual insects. The large difference in numbers between the two years can be attributed to the lower average temperatures of about 10°C. 

We also found that just 472 species were shared between the two years which is about 67% of this years catch. Initially we thought that this could be attributed to the fact that we had a lot of schools participating for the first time and also that our catchment area grew quite a bit. However, when looking at a handful of schools that participated both spring programs we still found many different species. There still is a chance of some data artifacts but one possible explanation might be the delay of this years' spring. Given that some arthropod species only have a lifespan as adults every shift even if it is just by a week or two might make a huge difference in the species composition of a given region. This year’s spring began about 1-2 weeks later than last year which might explain why we found so many different species in both years even at schools that participated both times.

This project is unique in many respects. Firstly, it is a great discovery based science project for classrooms in both elementary and secondary schools. The teacher and student feedback is very positive and the fact that with the help of BOLD we can give credit to each participating group for their contribution to scientific knowledge, is invaluable. 

Here an example for a species collected both in spring 2013 and spring 2014: 

Pear thrips are an invasive species from Europe. They arrived in California the early 1900’s and are now be found throughout most of the USA. They are tiny, measuring only 1.2 to 1.7 mm long, with brown-black colouration, two pairs of wings, and rasping mouthparts. They use these mouthparts to cut open leaves and buds of hardwood trees so they can feed on plant fluids. Last years collection of pear thrips by the School Malaise Trap Program marked the first time they have been barcoded from a Canadian location. They were found in 53 out 81 traps. This was a very interesting discovery last year and we speculated if it could signal a threat to Canadian forests – in the late 1980’s pear thrips were responsible for damage to 1.3 million acres of Pennsylvanian forest. This year we found this species in 45 out of the 58 traps, over 320 individuals in total. Interestingly it is thought that outbreaks of pear thrips are directly related to warm, dry spring weather that results in early budbreaks. The fact that we again found so many of them despite cooler temperatures and a long winter is puzzling. Natural Resources Canada considers these data as important and will include all locations (=schools) in their occurrence map for this species. Now, that's what I call a valuable contribution by the participating classrooms.

Open Access: The Bouchout Declaration

Last Thursday the Bouchout Declaration on Open Biodiversity Knowledge Management has been launched at Bouchout Castle in the National Botanic Garden Meise, Belgium. The goal of the Declaration is to foster international collaboration in biodiversity research by implementing principles of open access and regular readers of this blog know that this is very close to my heart.

The Declaration targets the need for data to be openly accessible, so that scientists can use the information for new types of research and to provide better advice. Currently, data may be prevented from becoming open or usable because of copyright оr concerns of institutions holding data, or because it is not available in a form that can be easily managed in digital form. The Declaration identifies mechanisms to structure open data so that they can be aggregated, queried and analysed on a much larger scale than was previously possible.

57 organizations and 58 individuals signed the Declaration, including some of the largest natural history institutions like Kew, Naturalis, Museum für Naturkunde Berlin, Botanischer Garten und Botanisches Museum Berlin, Harvard MCZ, California Academy of Sciences, InBIO and the Brazilian Virtual Herbarium of Flora and Fungi.

All signatories encourage an overarching approach to Open Biodiversity Knowledge Management based on the following fundamental principles:

• The free and open use of digital resources about biodiversity and associated access services;
• Licenses or waivers that grant or allow all users a free, irrevocable, world-wide, right to copy, use, distribute, transmit and display the work publicly as well as to build on the work and to make derivative works, subject to proper attribution consistent with community practices, while recognizing that providers may develop commercial products with more restrictive licensing.
• Policy developments that will foster free and open access to biodiversity data;
• Tracking the use of identifiers in links and citations to ensure that sources and suppliers of data are assigned credit for their contributions;
• An agreed infrastructure, standards and protocols to improve access to and use of open data;
• Registers for content and services to allow discovery, access and use of open data;
• Persistent identifiers for data objects and physical objects such as specimens, images and taxonomic treatments with standard mechanisms to take users directly to content and data;
• Linking data using agreed vocabularies, both within and beyond biodiversity, that enable participation in the Linked Open Data Cloud;
• Dialogue to refine the concept, priorities and technical requirements of Open Biodiversity Knowledge Management;
• A sustainable Open Biodiversity Knowledge Management that is attentive to scientific, sociological, legal, and financial aspects.

The Declaration remains open to sign. You might want to consider discussing its principles and their implementation and ultimately to sign it.

Barcoding snakeheads

Snakeheads are freshwater fishes with the ability to breath atmospheric air through some chambers that are located behind their gills.The group is split into the two genera Channa (native to Asia) and Parachanna (native to tropical Africa). Some snakeheads are small fish with a body length of 15 cm, but most of them grow much larger (up to 2 m). All Channa and Parachanna are fish-eating thrust predators with pretty sharp teeth. I can attest to that as I got bitten by a blotched snakehead (Channa maculata) once. It was painful, a bit bloody, but the most remarkable thing was that it was just a juvenile probably not larger than 10 cm. Adults of this species have been reported to grow as large as 1.5 m.

The smaller snakehead species and juveniles of some larger species are available to hobbyists through the aquarium fish trade. Especially some of the juveniles of larger species are very colorful which makes them a target for many hobbyists but there lies the problem. One day the fish outgrows any regular tank and the owner is looking for ways to get rid of it. Unfortunately most just bring the animals to a nearby pond or lake to release them and because of this, introductions far beyond native ranges have occurred. 

Some species are already established in North America while others have been captured from natural waters of the United States and more recently Canada without evidence of reproduction and likely represent released aquarium fishes. In addition to that snakeheads at or near sexual maturity are being sold alive in ethnic food markets as several species are highly valued as food fishes within parts of their native ranges.

Here a little video about snakeheads. It is already seven years old and exaggerating but that has become rather common in networks such as National Geographic or Discovery. Nevertheless, it shows why these fish are so successful once introduced.

And why am I talking about snakeheads today? Well, we just published a paper on DNA Barcoding of snakeheads and it is time for some self-promotion:

The objectives of this study were to assemble a library of DNA Barcode sequences derived from expert identified reference specimens in order to determine the identity and aid invasion pathway analysis of the non-indigenous species found in North America using DNA Barcodes. Sequences were obtained from 121 tissue samples representing 25 species and combined with public records from GenBank for a total of 36 putative species, which then partitioned into 49 discrete haplogroups. Multiple divergent clusters were observed within C. gachua, C. marulius, C. punctata and C. striata suggesting the potential presence of cryptic species diversity within these lineages.

Any utilization of DNA Barcoding needs a reference library and the establishment of one for snakeheads was our primary goal. During the process we discovered some cryptic diversity in some species and the next step will be to look closer into this and describe new species where appropriate. However, species listings such as FishBase and Catalog of Fishes currently list about 38 species for Channa and Parachanna which means that we covered most of them with our work. All species that are currently listed as introduced or potentially invasive species are covered.

The barcode data from this work could also inform the development of species-specific PCR primer and probe sets for the detection of environmental DNA for some of the known invasive species. This would greatly help conservation management with the detection of non-native and potentially invasive species without the need to catch any specimens.

New Malagasy Centipedes

Madagascar, the world’s third largest island, is famous for its endemic fauna and flora. More than 80 percent of Madagascar's ~15 000 plant species are found nowhere else in the world, including five entire families. Lemurs have been characterized as "Madagascar's flagship mammal species" by Conservation International and there are about 100 known species all endemic to the island. The list goes on and on. 60% of the bird species can only be found on Madagascar and about 99% of all the frog species (more than 300). Although invertebrates remain poorly studied on Madagascar, researchers have found high rates of endemism among the known species, e.g. all 650 species of terrestrial snail are endemic, over 90% of the ants as well.

Some millipedes also represent quite charismatic invertebrate endemics of Madagascar. These include the large-bodied, strikingly red-black colored so-called Fire-Millipedes of the order Spirobolida , and the giant pill-millipedes, locally called ‘Tainkintana’ (star droppings), reaching the size of a small orange or a tennis ball when rolled-up. The giant pill-millipede genus Sphaeromimus is a rather unusual representative of the order. One characteristic of the genus is the presence of well-developed stridulation organs which means these animals produce sound by rubbing together certain body parts. These stridulation organs are still not well understood, but may play a role during courtship and earned the genus the name chirping giant pill-millipedes.

An  international team of researchers has now published an integrative inventory (morphology and DNA Barcoding) of chirping giant pill-millipede species in Madagascar which revealed seven new species, many of them microendemics. These microendemics that can only be found in small forest fragments, less than a few hundred meters long and wide, are very likely threatened by ongoing rainforest destruction. 

Since the arrival of humans around 2,350 years ago, Madagascar has lost more than 90 percent of its original forest. This forest loss is largely fueled by traditional slash-and-burn agricultural practices that had been already used by the earliest settlers. The extensive habitat destruction, hunting, and harvesting for the ornamental animal trade have threatened many of Madagascar's endemic species or driven them to extinction, e.g. at least 17 species of lemur have become extinct since man arrived on the island. 

The newly discovered millipedes might vanish very quickly. One of them (Sphaeromimus lavasoa), is restricted to the Lavasoa Mountain, which is covered by an isolated, slightly larger than 100 hectare, rainforest remnant, which is famous for the recent discovery of a large scorpion as well as a dwarf lemur species.

Another new species (Sphaeromimus saintelucei) is probably the most endangered millipede on Madagascar. It was found in a fragment of the Sainte Luce littoral rainforest characterized by its laterite soil that is now so small that no lemur or other large vertebrate species can survive in it. It is also home to another species (Sphaeromimus splendidus) also believed to be a microendemic. Despite their close proximity, both species are not even closely related. They are only found in two very small rainforest fragments which are currently threatened by a titanium ore mining project. There are intentions to designate and manage conservation zones but current plans include only one large fragment that might not even include the last refugia for these species

Friday fun

Just a few good old DNA fun cartoons for the end of the week. Have a great weekend!

PhylAphidB@se

Aphids (Hemiptera: Aphididae) constitute a diverse group (about 4800 species) of plant-feeding insects. They occur mostly in temperate regions and European aphids account for one third of the world’s fauna, with approximately 1400 species. The intricate life cycles of aphids and their close association with their host plants, polyphenism and ability to reproduce both asexually and sexually make these insects interesting systems for studying many issues in evolution and ecology, but they also make species identification challenging.

Indeed some intriguing facts on these fascinating animals. However, most importantly Aphids are small insects that are often transported around the globe, constituting an invasive threat to native and cultivated plants. Actually they are considered one of the most serious agricultural pests of temperate regions because they cause direct damage by feeding on phloem and because they can act as vectors of many plant viruses.

Unfortunately, the range of continuous morphological variation in aphids is probably wider than in any other insect group which makes any accurate identification very difficult. Researchers also know of the occurrence of different morphs on different host plants and at different times in the year. A number of genera can't be identified by using morphology alone. Researchers need to include information on host-plant association to arrive at an accurate identification. There are also considerable gaps in our knowledge which is e.g. illustrated by the fact that for the genus Aphis, no taxonomist has yet succeeded in writing a comprehensive dichotomous morphological key that effectively separates all the species of a given local fauna.

A new study by a group of French researchers from the Centre de Biologie pour la Gestion des Populations (CBGP) and the Institut national de la recherche agronomique (INRA)  is now showing how to use DNA Barcoding to overcome these obstacles. They created the first European aphid barcode database including about 274 species:

These data confirm that COI barcoding is a useful identification tool for aphids. Barcode identification is straightforward and reliable for 80% of species, including some difficult to distinguish on the basis of morphological characters alone. Unsurprisingly, barcodes often failed to distinguish between species from groups for which classical taxonomy has also reached its limits, leading to endless revisions and discussions about species and subspecies definitions. In such cases, the development of an effective procedure for the accurate identification of aphid specimens continues to pose a difficult challenge.

The authors also suggest to establish a host-plant herbarium linked to aphid voucher specimens, which would allow the confirmation of aphid species identification when aphid morphology is not sufficient. Aphid taxonomists are, by necessity, also “amateur” botanists, they are not specialists in plant systematics. In situations in which the identification of the aphid is dependent on correct host-plant identification, the frequency of misidentification may be increased further. Once both aphid species and host plant species have a proper DNA Barcode designation they can be used for future reference.

Invasive vs. endangered

Resolving conflicting ecosystem management goals—such as maintaining fisheries while conserving marine species or harvesting timber while preserving habitat—is a widely recognized challenge. Even more challenging may be conflicts between two conservation goals that are typically considered complementary. Here, we model a case where eradication of an invasive plant, hybrid Spartina, threatens the recovery of an endangered bird that uses Spartina for nesting.

Efforts to eradicate invasive species increasingly occur side by side with programs focused on recovery of endangered ones. But what should resource managers do when the eradication of an invasive species threatens an endangered species?

The California Clapper Rail (Rallus longirostris obsoletus) is a bird found only in the San Francisco Bay. It has developed an interest in an invasive salt marsh cordgrass called hybrid Spartina and came to depend on it for nesting habitat. Its native habitat had slowly vanished over decades, largely due to urban development and invasion by Spartina. Spartina alterniflora was introduced to the Bay in the mid-1970s by the Army Corps of Engineers as a method to reclaim marshland. It hybridized with native Spartina and invaded roughly 800 acres. Eradication of hybrid Spartina began in 2005, and about 92 percent of it has already been removed from the Bay. 

In 1998 two researchers stated that the San Francisco Bay is perhaps the most invaded estuary in the world. They identified a total of 234 exotic species established in the ecosystem, including plants, protists, invertebrates, and vertebrates. Most of those were transported in ballast water that was purged in the bay making the estuary a very good example for the extend of introductions of new species.

In a new study researchers at the University of California, Davis examined the described conundrum now taking place in the San Francisco Bay. Their results showed that, rather than moving as fast as possible with eradication and restoration, the best approach is to slow down the eradication of the invasive species until restoration or natural recovery of the system provides appropriate habitat for the endangered species:

We show that the optimal management entails less intensive treatment over longer time scales to fit with the time scale of natural processes. In contrast, both eradication and restoration, when considered separately, would optimally proceed as fast as possible. Thus, managers should simultaneously consider multiple, potentially conflicting goals, which may require flexibility in the timing of expenditures.

Given how much the eradication has already progressed these results should be put into action rather swiftly.