¿Do you believe they’re the same?

According to the SER, ecological restoration is “an intentional activity that initiates or accelerates the recovery of an ecosystem with respect to its health, integrity and sustainability”. That is, ER is an empirical endeavor full of practical know-how.

Restoration ecology on the other hand is the theoretical or scientific corpus associated with the restoration practice.  But they’re not the same “ting”. You may believe that the academic expert is likely to restore some land but give him the responsibility and he won’t have a clue what to do about it.

Bradshaw has stated that “restoration is an acid test our ecological understanding”. I  agree but restoration practitioners don’t work applying abstract theories of nature but following a simple heuristic that is usually forgotten: Copy nature.

We are relying on phenomenology, that is, the observation of empirical regularities to do our job. These regularities have now become part of the ecological corpus under names like the theory of succession which we use because we are educated.

I’m always amazed how rural people understand restoration very well.  They tell you things like “Sir, I believe we should start using this plant it helps the soil after it’s gone and other plants to germinate” without any mentioning of succession or whatever.   But they know what to do.

They know a lot more than the ecological restoration theorist with a PhD and dozens of articles who has never worked in a single project and has never planted a single tree. I stay away from people who never get their hands dirty.

My pledge is for a bottom-up approach were theories and articles come from the practice of restoration, not the other way around. I’m against the academics that are lecturing-birds- on-flying  and teaching-mother-nature-ecology and can’t do anything practical because they blew it up.

These people are trying to outsmart nature driven by naive rationalism, and only achieve failure through exposure to massive potential mistakes like introducing invasive species and worsening the soil condition.

There is a logic to natural things that is much superior to our own, and nothing is more true that in the complex realm of ecology. We must fight against the notion of modernity and the believe that we have a large-scale understanding of the environment and we can control it.  Because we don’t.

But we have enough knowledge to help overcome the barriers to succession and let nature do the rest of the job.  That’s what real practitioners do.

Pd. For a more academic discussion read  Clewell and Rieger (1997) ; Cabin et al. (2010)

The christmas bird count is a wonderful activity promoted by the Audubon Society  that takes place every year from December 14 to January 5, where experienced and amateur birders host the  longest running citizen science survey in the world.

The census helps for conservation purposes documenting the change in bird populations and distribution of species over the years. All individuals heard or seen are recorded, compiling a huge database that helps to answer many research questions.

The history of the counts is really interesting. In America there was a tradition of hunting birds in christmas at the end of the XIX century, but the conservation movement begun questioning this activity seriously,  and it was the legendary ornithologist Frank M. Chapman, in the recently born Audubon society who proposed to count birds instead of hunting them.

On december 25 of 1900,  the first christmas bird count  took place, with 25 localities, 27 participants, 90 species  and 18500 birds counted.

I’m proud to say that  Colombia has been a leader in South America promoting the CBC, with the biggest numbers in terms of volunteers and census circles. The number of christmas bird counts has increased  steadily over the years in almost and exponential way. The counts are organized by the RNOA (Red Nacional de Observadores de Aves) and SCO (Sociedad Caldense de Ornitología) in our country.

I participated in the 2012 christmas bird count in the IBA (Important Bird Area) of San Antonio-E l km 18. It was tremendous success.  The count was organized by the folks at Mapalina Birding Tours and Colombia Birdwatch, composed of a team of people with great expertise in the area. The count started at 6:00 am and i was happy because i’ve always been an early bird so I had little trouble.

We recorded 85 bird species and  the list included the colombian endemic and magnificent multicolored tanager (Chlorochrysa nitidissima), and other good looking  tanagers as the blue-winged mountain tanager (Anisognathus somptuosus), the Beryl-spangled Tanager (Tangara nigroviridis), the golden tanager (Tangara arthus) among others.

Also relatively big and cool-looking birds were saw as the read headed barbet (Eubucco bourcierii), the Andean motmot (Momotus aequatorialis) the crimson-rumped toucanet (Aulacorhynchus haematopygus), the collared trogon (Trogon collaris) and the Colombian chachalaca (Ortalis columbiana).

The count also included rare sighting of two notoriously difficult to see neotropical birds: The Andean solitaire (Myadestes ralloides) wich was pretty active foraging on bushes, and the Chestnut-breasted Wren (Cyphorhinus thoracicus), spotted singing in a
branch near the road.

Hummingbirds are also a delight to see and we were not short with sightings of the Tourmaline Sunangel (Heliangelus exortis), the long tailed Sylph (Aglaiocercus kingi), the booted racket-tail (Ocreatus underwoodii)  the small purple- throated woodstar (Calliphlox mitchellii) and others. Flycatchers, birds of prey, parrots, antbirds and other groups were also seen and recorded.

At noon after the count was over we went to a beautiful house in the km 18  to have a  ”fiambre valluno”, a delicious typical dish wrapped in plantain leaf with rice, beef, pork, chicken and yellow potatoes. We then shared our experiences and had a terrific evening. I haven’t missed a christmas bird count since 2010 and i am forward to look at the next year count.

There is no institution more important for botanists than the herbarium. In layman terms, it is a collection of dried plants  and you can think of it as a plant library. It provides information and data on everything related to plants, and documents the incredible plant biodiversity on earth. It is the center of all botanical activities and at it’s core we find taxonomy to be the most prominent of them all. The herbarium is the primary reference source for the taxonomist, were floristic works and monographies are made.

Herbariums are composed of herbarium specimens, which not only include the dried plants mentioned earlier but  also pollen, fossils, wood samples, dried fruits, photographs and drawings.  It is important to include all of them because they provide a more complete description of the plant world, with more data to work. A collected plant only has value if it has great information on it, and this information is stored in a way accesible to researchers, as in a huge database.

Herbariums are usually the place to indentify plant species or discover new ones to science, they provide material for making taxonomic revisions, to measure species morphology, and help as a repository for new collections of plants.
Also really important is they are a repository of type specimens, on which the scientific name of a taxon is formally attached.

I have been associated with the herbarium in my university  (abbreviation: ICESI) since it began two years ago. I’m skilled in it’s operation and maintenance, and i’m currently in the position of herbarium assistant. Most important to me, is that i have learned in the field trips how to properly collect plants, how to press them, and register the neccessary information to later store them in the herbarium. This is key since i want to be part on plant biodiversity surveys across Colombia and the tropics.

Caves are a fascinating subject, and through history they’ve been feared, respected, admired but never ignored.  However, it’s biota went a long time unnoticed because naturalists reasoned the conditions were tough to have life in them.  But everything changed with the discovery in 1700 of an eyeless salamander in Eslovaquia when scientists begun to question what else could be find there. Bioespeleology was born. Also,  with a more deep understanding of caves, it is becoming clear that most of them (specially limestone and other solution caves)  are like terrestrial environments, with spatial heterogeneity and stable conditions to sustain life.

Caves thrive in biodiversity. Let’s make a quick recount, or it will take forever. Insects are the most representative of all taxa, and coleoptera the most diverse within them. Mollusks, chilopods, diplopods, and a huge arrray of arachnids are also present. The crustaceans are the  more diverse aquatic invertebrates, with a big representation of amphipods and isopods. Now, in the vertebrate side fish comprise the mayority of the diversity. Also we can find other vertebrates like salamanders, bats, reptiles like snakes, and birds like the curious oilbird Steatornis caripensis.  Now, you must be thinking that these animals should be different from the cave outsiders, and you are right.

Let’s consider now how an animal living in the caverns would look like:
you could think that in the darkness you don’t need eyes or fancy pigmentation, and you are right. Because of the lack of light in caverns there’s no need for any of these. They should be small because of the physical limitations of most caves, but they would have big appendages with more complex chemo- and mechanosensors to compensate for the lose of sight. All of these characteristics are called troglomorphisms.

On the other side,  they’re metabolism should be reduced in order to survive more days without food, and the lipid storage increases to give energy to the animal while he’s not eating. What about their behavior? in the darkness most animals would become opportunistic and work on their own. Aggregation and aggresion are out of the way.

Have something in mind: Across different species some will or not have these characteristics.Recent advances have clearly show that we can not talk of an arqueotype of the hypogean (underground) organisms. Take fish for example. A third of all hypogean fish are completely pigmented and have well developed eyes.

For an easy classification of animals living in caves, researchers have deloped a useful vocabulary.We got the troglobionts; exclusive from caves, troglophyls, that spend part of their lifes in caves and trogloxenes, which habit the caves in a temporal or accidental manner. Also it is common to refer to the aquatic species as stygobionts.

The key to understanding the adaptations to caves resides in a high phenotipic plasticity. Experiments have been conducted where a hypogean larval fish is subjected to ligth and darkness for 30 days. In the darkness, she will have not eyes. But in the presence of light, she would get some big pair of eyes. This ability for gene expression is the core aspect to an evolutionary answer for the colonization of caves.

So how the hell did these animals ended up living in the caves? Do they have some kind of deal with He-Who-Must-Not-Be-Named? Well, for long time the most accepted hypothesis was an accidental colonization, but now we know animals go to cave in response to selective pressures like for seaking shelter and escaping from predators like the bat fish Noctilio leporinus.

Caves are really complex and i have just touched the tip of the iceberg. My message is that they have an incredible biodiversity, which needs a lot more studies and discoveries, and that we need an integrative approach to study them, just like we do in terrestrial environments.

A typical 1ha of tropical rainforest may contain about 700 different plant species. Now, if you want to identify them, unless you are Alwyn Gentry that is a big problem.  A taxonomist is a weird creature with almost magical knowledge into the names of plants, and has highly specialized skills and vocabulary.

For a diverse set of conservation and ecological problems, the starting  foundation is always to  identify species correctly. Nothing is more boring than papers referring to species as  ” Bignoniaceae sp.1 , Bignoniaceae sp.2 etc”. Believe me, i have read a lot of them and you stay with the feeling you got nothing of value.

So.. what is the solution? DNA barcoding. It’s  like giving every species a unique genomic signature. Basically what you do is take a short, standardized  and universal portion of the  genome, which can satisfy the criteria of having high variation among species but low variation in individuals. Then by sequencing, every species will have a unique ADN identifier.  For animals the choice is a portion of a mitochondrial gene for the cytochrome c oxidase (COI). Plants don’t have a unique barcode yet but a combination of two genes have been suggested, and the rbcL/ trnH-psbA combo has the best results for tropical plants.

Just imagine, being able to identify and name every plant species at your side,  and animals also. Currently samples must be taken to laboratories for correct identification , but portable barcoding devices will be ready in the near future. You will feel like Ash with his pokedex toy.

One of the biggest advantages of barcodes is that you can correctly identify plant species with fractions of the complete individual, name them wood, leaf or flowers, or seeds. In order to give every plant  it’s unique identifier, the best practice is to sequence type specimens from recognized herbariums.

A big challenge now is to integrate DNA and traditional taxonomy in order to generate a robust approach for the description and delimitation of species.  This is the reason DNA barcoding won’t replace the charismatic taxonomist, there is more need of them than ever. We need them to correct for errors in the sequencing, for describing new species, and to keep feeding the barcode databases like The Barcode of Life Data Systems (BOLD).

Please keep an eye on the advancements on DNA barcoding. Like John Kress says, it can be a windfall gain for tropical biology.

Here we have two of the best software for measuring biodiversity parameters to assess species richness, like the famous accumulation species curve, and lots of indexes like the Shannon-Wiener, Simpson and Margalef. Also you can measure B diversity with the Jaccard similarity index and other indexes. EstimateS has the Chao-Jaccard Index, which according to Chao et al. 2005 “has been shown to reduce substantially the negative bias that undermines the usefulness of traditional similarity indexes, especially with incomplete sampling of rich communities”. I have reviewed this paper and the statistics look robust.

I find that Biodiversity Pro is more intuitive and you can get your indexes really fast. Estimate S is more tricky and you need to get used to the way to enter information, but once you get it’s easy as well. One thing you must remember is that none of this software is useful if you don’t have a crystal clear view of what you want to do with the information obtained. Also you need to be confortable with the terminology and how the indexes work. If you know this stuff, then working with any of these programs is easy cake.

What I don’t like about Biodiversity pro though is that it hasn’t been updated since 1997. And that’s a long time. By contrast Estimate S is and the last version 8.20 is from 2009. I feel more confident using a software that is obvious the developers are paying a lot attention to it. I suggest you try both programs and take your own decision.

 Ok.. .ready?

Here you can download Estimate S (Requires prior registration)
http://viceroy.eeb.uconn.edu/estimates/EstimateSPages/EstimateSRegistration.htm

And here is the link to Biodiversity Pro
http://gcmd.nasa.gov/records/NHML_Biopro.html

A biodiversity hotspot is a geographic area that due to its physical and biological characteristics has high levels of plant endemisms (1500+ vascular plants, 0.5% of the worlds total) and  has to have lost at least 70% of the original habitat. Currently there are  34 biodiversity hotspots and most of them are tropical, but some are not. Whoever the ones in the tropics have the highest rankings in endemisms.

Look at the map closely and you will see that Colombia is practically a hostpot all by itself.  We have the biggest biodiversity hotspot which is the Tropical Andes, and we also have the  Chocó Biogeographical Region.

The polar regions contain no hotspots, and a good example of a temperate hotspot is the Mediterranean Basin or the Cape Floristic Region of South Africa.

 Hotspot science is really interesting. In about only 2.3% of the worlds land surface, these areas held together at least 42% of all terrestrial vertebrates and 50% of all plant species.  If you thought Carlos Slim was a good example of wealth concentration, think again.  Also hotspot science is continuously advancing and the number of species is likely to go up. For example we know now that 29%  of the world’s freshwater fish species are hotspot endemics, with 55 percent of species occurring.

Not only biodiversity hotspots hold an incredible diversity of life; researchers have found there is a co-occurrence of linguistic and biological diversity, and hotspots hold at least 70% of all languages on earth. Human health depends on biodiversity and  the hotspots provide hydrological control, atmospheric regulation , food security, dietary health protection against infectious diseases among many others.

I want to examine closer the hotspot criteria here. At the biological component the endemisms are measured with plants, not with any other life group. And you see that plant diversity is highly correlated to animal biodiversity. There is more food to chose, more niches, and more diversity of animal life. Also because these areas are severely threatened, they are perfect for conservation purposes. And there is a big conservation challenge.

As you can imagine, there is a huge problem with threatened species.  51% of mammals, 73% of birds and 77% of  amphibian species  are hotspot endemics. By the way,  the most threatened species are in the tropics, which are also the center of violent conflict, making the work very difficult for researchers and conservationists alike.

It’s just kind of hard to speak to people in arms and conservation depends primarily on the good will of people.  Nevertheless, careful regional planning has giving it’s fruits and the dedicated work of Conservation International, who work to stop the lose of biodiversity in the hotspots by defining targeted conservation outcomes like  ”Areas Protected” and “Corridors consolidated” outcomes.

 Biodiversity hotspots are not the ultimate system for assessing conservation priorities in our planet. We got for example WWF Ecoregions for conservation, and they include 4 terrestrial, 3 freshwater, and 4 marine habitat types.  However, i’m a huge fan of the hotspot concept and the work of Conservation International.  And because i’m most into plants, i find hotspots a real opportunity to me.  I would love in the future to do some work in these areas and maybe visit them all. I’ll keep you informed.

Biodiversity surveys are the most direct way to assess the species diversity of a given area, and data collected with them is priceless. It can help us describe the composition and structure of a landscape, to evaluate conservation priorities,  and to make comparisons and analysis for ecosystem management and diverse disciplines like ecology, biogeography and systematics.

There are three elements to take into account for a good design of a biodiversity survey:

1. The objective of the survey; it must be crystal clear, because determines the methods for the survey, the geographical area to study, and the sampling effort.

When you do a species diversity survey mostly the method is to work  with plots or transects that allow to obtain information about the characteristic of an area , without the need to study it completely because it will take an eternity, wastes time and money, and its not necessary because a good old statistical fact is that a well taken sample is representative of the whole population.

2. You must select which taxonomical groups are appropriate  and ensure the implementation of a standarized methodology of sampling for each one of them.

The use of indicator groups is a key strategy and mostly in tropical areas these area  birds, plants and insects.  They are indicators because they can provide good information about the conservation status of an area and they have different ecological requirements.  Insects are a huge group and the survey efforts are focused on scarab beetles (Coleoptera: Scarabaeidae) , ants (Hymenoptera: Formicidae) and butterflies (Lepidoptera: Hesperioidea, Papilionoidea)

Also they are good indicator groups  because their taxonomy and natural history is well known, they are highly diversified and can be find in different ecosystems,  and they are abundant, it’s easy to observe them and manipulate them. Imagine using mammals as indicator group,  it would be a nightmare! They are so hard to work with, manipulating them is out of the question and to watch some of them is almost a miracle. For example, there is people who live in areas spectacled bear (Tremarctos ornatus), but they’ve never seen one.

Plants obviously are the top choice and every biodiversity survey must include plants.  The vegetation is the first thing to mention when describing a landscape, ecosystem or an area. With plants also  it’s possible to extrapolate and use them to tell which other taxonomical groups will inhabit the zone. Off course great care must be taken.

3. There must be an agreement in how to generate, capture and organize information so that it’s easy to use in the analysis.

It’s imperative to standardize how the data will be handled and also it has to be easily accesible and intercheangable. User friendly bioinformatic tools are becoming extremely neccessary. The original information will be interpretated accordingly to the researchers objective , but it’s vital to conserve the raw original data, as it can be used for other purposes later on.

Another aspect is that always, always there ought to be some sort of physical evidences.  Plants have to be collected and taken to a herbarium. With birds you can record their songs and prepare their skins and  insects are easy to preserve. The objective is to guarantee the availability for long term of these collections (decades and even centuries)

So as you can see a biodiversity survey not only includes field work but a lot of planning to ensure it’s worth it. A good survey, when executed properly,  is the first tool to use in a biodiversity assessment.

According to my college textbook, ecology is the scientific study of the interactions that determine the distribution and abundance of organisms. This is a really interesting subject and it becomes even more interesting when you ask why most of the species on earth are concentrated in the tropics. The discussion can start by the fact that  geographic areas has a fundamental role over biodiversity, and that’s why species diversity in the tropical zones is so much greater in respect to the temperate regions. It’s sad to realize that even when we want to,  richness is not distributed equal.

The geographic area influences directly with variables such as temperature, humidity and luminosity that determine the tolerance limits of the species. We can also find that the tropics hosts a huge array of biodiversity because these variables are more stable in the majority of cases. Also life has been able to diversify in the tropics  due to the abscense of great geological perturbations, like the glaciations that affect the temperate zones. When a glaciation strikes, it leaves almost nothing and life has to start again with processes of primary succession.

Now from studies in ecology we know that most species have a very narrow distribution, and that they’re not abundant. The contrary is true for widespread species that have high population densities. For a mundane example, rats are superabundant and you can find them everywhere (chances are there is one of them watching you right now)

I mention this ecological observation so you can understand better what is happening in the tropics.  We have tons of different species, but they are distributed in really specific areas. That is why deforesting  say, 10 hectares of tropical rain forest is devasting.  You could easily have lost some species in that process, because they’re distribution is so limited.  Deforestation in a tropical rain forest is a genocide to nature.

One of the biggest challenges in building a career in biodiversity is the ability to quickly and correctly identify the plant species that you encounter in the field. If you need to go to an herbarium, then you’re screwed. I know this because i happen to have a great botany teacher in my college, his name is William Vargas. When i go with him on a trip, he can identify almost all plant species, even down to species level, with the blink of an eye. Off course there are some identifications that needs to be done in the herbarium, but only in special cases.

Studies in vegetation are so important because they are the support for planification, management and conservation of tropical ecosistems. And remember that the tropics comprise almost two thirds of all vascular flora. Colombia itself has about 30,000 plant species. This is why learning to identify plants is not an easy task.  There are at least 250 plant families in the neotropics only. Some very different from each other. Some perplexingly similar. By identifying a plant to family level then it’s easy to go down to the genre and species level, whoever  i would say it’s best to identify to genre level because with the APG system some families are constantly changing.

I’m completely determined to be able to identify tropical plants (currently i’ve learned some 25+ families), and luckily I’m in the right position to get the job done:

1. I live in the tropics (Colombia) and travel a lot.

2. I’m an assistant at ICESI herbarium and have access to the 20,000+ plants we currently have there.

3. I have books great available

-Alwyn Gentry’s excelent book:  A Field Guide to the Families and Genera of Woody Plants of North west South America : (Colombia, Ecuador, Peru).

-And my favourite, my teacher’s own book,  ”Guía ilustrada de las plantas de las montañas del Quindío y los Andes centrales” which is a guide to the botany of the Andean mountain regions of Colombia, containing at least 206 plant families.

4. I will be taking  a course in plant taxonomy and systematics with my teacher  and that will be my catapult to reach my objective. (i will keep you informed)

So, that’s the tropical plant taxonomic challenge i’m up to right now, and i can’t see the day when i go to the field and have cracked the code to identify all  plant species, the way Neo sees the matrix. Meanwhile, i have to enjoy and honor this journey.