It depends on the scale of your study. If the area is large enough to fit a few pixels of a high resolution satellite data then use that as a 1st study. Homogeneous NDVI signature will indicate a low biodiversity and vice versa.

Record different species under following headings;

1. Plants Biodiversity

2. Animal Biodiversity

Under Plant biodiversity, you will need the assistance of a plant taxonomist and will have to conduct surveys throughout the year or during four seasons to record the plant species of all seasons.

Under Animal biodiversity, you will need the assistance of;

a. A specialist of invertebrates

b. An Ichthyologist

c. A Herpetologist

d. An Ornithologist

e. A Mammalogist

If you are planning to perform all the jobs yourself then you will have to collect the identification and taxonomic keys for all the groups. You will also need patience, practice and determination to produce some authentic data. You must consult all the recorded information along with the available evidences with some seniors. 

It is a nice question and best fit for the Arunachal Pradesh or Eastern Himalayan Biodiversity hot spot. There is much to do so explore the biodiversity of this region. Although some efforts in the round but it is meagre. I think to explore the biodiversity of such region we need to collaborate research works by identifying experts from different parts of the world as well as different disciplines and carry out extensive field tours by segregating the areas into micro areas. Starting with a particular area covering up the whole state or region and archiving the recorded or collected information.

First In my opinion go for status mapping ( Using Rs and GIS) of that area to see the richness of the region than explore for other parameters 

Based on the previous comments, it seems to me that your first step is to decide at what level of diversity you want to work, meaning if you want to work at ecosystem or at species level (I will leave the genetic level of diversity out, because I cannot help on that level). So, if you want to work at ecosystem level, you may want to use surrogate information such as remote sensing information, as well as thematic information such as geology/geomorphology maps, vegetation units maps and land-cover maps and find adequate ways to combine these in order to have a notion of the mosaic of ecosystems at landscape scale and thus, trying to infer its biological diversity (there should be a lot of studies done using a similar approach). On the other hand, if you want to work at species level, you can try to look for good studies on Rapid Biodiversity Assessments, such as the ones commented in: http://www.fieldmuseum.org/science/blog/rapid-inventories (the one I knew was the Cofan (Equador) one). Basically you choose about five groups of well-known living beings (tipically vascular plants, mammals, birds, reptiles and amphibians and butterflies) and prepare an intensive field campaign in order to collect and identify them, and later synthesize and compare with similar areas.

In my opinion  you need to strat with plants richness and distribution so you can for (GIS) and for Animal you need to do alot of work because there is alot of groupe' it looked complicated so you we need to pricise the objectif of you reserch,

good luck

Considering the previous answers to your question, it make me think of the work of  Landscape Architect - Ian L. McHarg, that basically formed the fundamental thinking of 'layers' used in GIS mapping. In his book Design with Nature, 1967, he describe the steps to collect, evaluate and plan for ecological systems in a specific region. Going back to the principles of this process could help you frame your problem and put a 'boundary' around the scope of the work.

Phillip Roos..can u share me the link of Ian L. McHarg's work... specifically RS-GIS studies as a beginning is favorable but difficult to arrange for in a region that lacks basic infrastructure of lab setup. However, National Remote Sensing Agency maps can be of some help at this juncture. Apart from RS-GIS studies, I also welcome the comments pertaining to maintaining a record of different group of plants and animals, as discussed by Waseem... I also feel, choosing five groups of well-known living beings (typically vascular plants, mammals, birds, reptiles and amphibians and butterflies) and prepare an intensive field campaign in order to collect and identify them, and later synthesize and compare with similar areas, as discussed by Pedro as a systematic approach to the work

All of the above responses have excellent points and I hope that I don't find myself repeating anything. However, going off from what Pedro Miguel Ramos Arsénio said about deciding what level of diversity you'd like to work with, I think it would also be worth considering what you (or you and your research/field crew/stakeholders) deem to be important or valuable regarding biological diversity. What are you interested in? Are you interested in obtaining a snapshot of the biota, both flora and fauna, of this given area? Are there perhaps endangered/threatened species that are found here, or perhaps keystone species? Or are you interested in determining if there are any biota that could offer important medicinal goods? Or are you looking at biological diversity as an indicator, such as for climate change or other environmental variables? By extension, another question worth thinking about would be what sort of biodiversity would be of greatest interest- species richness (such as alpha, beta, gamma diversity), phylogenetic, genetic, genomic, structural, functional/functional-trait, etc. But, before deciding what measurements you'd like to take or what methodologies you'd like to implement, it's worth first taking the time to figure out what you and your stakeholders value in biological diversity. In other words, what sort of non-epistemic values are guiding your data collection and research efforts? From there on, it will be easier to decide what methodologies/measurements to use.  

Also an important question: who is going to identify your samples (if you are going to be sampling)? What kind of taxonomic expertise do you have or have access to?  Why are you doing the study? Your question is too vague for us to give much useful help. 

Brian... The region, I am newly posted is a majorly unexplored  biodiversity region.  We have no records, papers, documents; on what are the species available in different ecosystem levels; how common or exotic a particular species is to the region; whether endemic or invasive; whether threatened or extinct; whether available or introduced and so on. On behalf of our department, we feel the necessity to record the biodiversity of the region. However, as there cannot be a particular protocol of doing that and many options can be followed, as discussed above; the need of maintaining a register or record is of utmost importance... We will collect the samples separately of different floral and fauna species; and will send them to expert bodies for proper identification. This will help us in start maintaining a record. The different bodies will be Botanical Survey Of India, Zoological Survey of India, Bombay Natural History society and other regional offices of environment departments at state and national level. I was asking of a particular procedure/procedures followed in beginning such a study that will help us in proper collection, maintenance, identification and record maintenance as well as ease the task of the departments, as mentioned above, that will help us in doing the identification part. We will not get any experts from them for field protocols. We need to do the field part and send over to them for identification and record maintenance; a copy of which will be forwarded to our university department as well.

I completely agree with the comments made above. First you need to decide on which taxa/group you wish to start your work on. If you wish to make a complete inventory of the region, you need to consult several experts before drawing up a proper plan to document the diversity. A thorough consultation is required as you might unnecessarily waste your efforts due to a poor work plan.

Hi Joystu,

See work by Bill Magnusson and INPA (in Brazil) on the "RAPELD" system used in hyperdiverse tropical regions. 

See the "Biodiversidade e Monitoramento Ambiental Integrado" (english text togther with portuguese), freely available : http://ppbio.inpa.gov.br/livros

Plus you may want to look at the discussion we recently published which attempts to summarise some of the issues regarding how to sample when we are uncertain of present or future "biodiversity" levels:  http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0106150

Best,

Darren

Use a landscape approach, starting with indicator species, and measure alfa, beta and gamma diversity. This is a good starting point and will let you have a baseline for future monitoring. You can also correlate these parameters to landscape indicators, fragmentation, forest associations, geomporphological features or altitudinal gradients. Posting here my thesis in case you read spanish...

http://biblioteca.usac.edu.gt/tesis/06/06_3202.pdf

My advice here would be to favor the easiest ways to do so (data collection and analysis) in order for you to be able to replicate your approach and to develop a  monitoring approach. But before designing your activities, there are a few questions you need to address first. Then only, after you are clear on these questions, you can decide about what is the best approach for your BioD assessment:

• what are the questions you want to answer? What do you want to show? 
• what is your time frame?
• what resources are available: financial, human and time?
• is your team already trained or do you need external input? In this case which one?
• What is the size and accessibility of the area you want to cover?
• Is there a will/need to work with local communities?

I find it very informative to have a clear idea of waht we want to achieve before deciding for the activities you need to carry out. 

If you have yet definite at what scale you must to work, you are answers in the two preceeding comments (G. Steenbeecke, M. Ancrenaz). If your decided to work at a smaller scale (for instance one part of wild and/or cultivated surface into the perimeter of a village of your country, I can give to you some indications on invertebrate groups to work (insects, collemboles, enchytreids ...) for biodiversity in the soil, on soil surface and on cultivated/wild plants. André Panis [email protected]

Hi Joystu,

I agree with all the previous answers.

Even if environmental DNA sampling could be faster, and depending to your goal, I prefer to suggest a traditional study by collecting individuals on the field. More funding will be required if your wish to store and locally manage the collected material. All these material could be the base of very numerous and taxonomic revisionary works. But, this kind of study always need some dedicaced people to sort the material + a good network of proactive specialists to identify the specimens at the level fitting your needs. I take as example the work realized in French Guiana by the SEAG entomological association over more than 10 years with a network of over 70 experts (ZooKeys 434: 111-130 (14 Aug 2014) doi: 10.3897/zookeys.434.7582). This will take time but at low cost (collected specimens are mainly managed by each specialists and types always deposited in a national museum) and give nice results, discoveries.

Good Luck for your project!

Both the U.S. National Park Service Inventory and Monitoring Program and California's Natural Community Conservation Planning process have gone through this in the last 2 decades. In the National Park Service the goal was to document 90% of the vertebrates (mammals, birds, reptiles, amphibians, fish) and the vascular plants in each of the national parks. Invertebrates and non-vascular plants were saved for later. Mostly this was done by contracting with Universities, the U.S. Geological Survey, or other specialists to take a taxonomic group and combine museum record searches with exhaustive in the field searches using a variety of techniques. You have to make very sure your objectives are clear because many researchers find simply documenting the species in an area uninteresting from a research viewpoint and will try to add other goals.

In California Dr. Robert Fisher of the U.S. Geological Survey was frequently funded to do vertebrate inventories of newly designated conserved lands including small mammals, large mammals, reptiles, amphibians, fish, birds, and bats. So he trained up his people to do the variety of different tasks. He would be a good person to talk with.

If you decide to do the inventories yourself , you should consider at least consulting with professionals in the field and making sure you are implementing the procedures correctly. I know we had some problems in NPS with wondering if the "no detections" of some mammals that had historically been present in the park were due to their absence or to the methods being implemented by people who had never used them before.

Another option is to look at the National Geographic/National Park Service BioBlitz efforts that are going on in a different U.S. National Park each year leading up to our centennial. These are primarily public outreach events and are a lot of work but can yield some good results fast . Scientists in a wide variety of fields are invited to the park together with area schools and volunteers with the goal of inventorying as many of the species in the park ask possible in 24 hours. It can take months to over a year to get all the results back from the researchers, especially those identifying species under microscopes. You may document about 50% of your vertebrates and vascular plants this way so its not a very complete inventory. But its a way of engaging the surrounding community.

Good luck!

Andrea, This depends very much on the question being asked. If the aim is to maximize the detection of the diversity (richness) of species and or functional types or traits in any area using the most logistically cost-effective strategy then I would recommend the use of gradient-directed transects or gradsects. The statistical model underlying gradsects does not require randomized sampling, relying instead on purposive location of sites along key environmental gradients. The sampling strategy relies on the assumption that the distribution of biota is rarely driven by random events, being driven more by the nature of prevailing environmental gradients. The gradsect method uses a nested, hierarchical approach to site location. For the great majority of purposes it is generally much more efficient than resource demanding random sampling and far more cost-effective logistically.

There are now many studies available that describe the method and the outcomes. It is the preferred method for example, in the mainland USA for many biodiversity assessments and related management in National Parks. A Google scan will extract many more examples worldwide.

See Also: Gradsect and Field Sampling Plan for Big Bend National Park/Rio Grande National Wild and Scenic River. by USA National Park Service (NPS) 2012 (Book)   Product Details ISBN-13: 9781249375326 Publisher: BiblioGov Publication date: 9/13/2012 Pages: 184.

Gillison, A.N. (2013) Plant Functional Types and Traits at the Community, Ecosystem and World Level, in Vegetation Ecology, Second Edition (eds E. van der Maarel and J. Franklin), John Wiley & Sons, Ltd, Oxford, UK. Ch 12, pp.347-386. doi: 10.1002/9781118452592.ch12

Gillison, A.N., Bignell, D.E., Brewer, K.R.W., Fernandes, E.C.M., Jones, D.T., Sheil, D., May, P.H., Watt, A.D., Constantino, R., Couto, E.G., Hairiah, K., Jepson, P., Kartono, A.P., Maryanto, I., Neto, G.G., Neto, R.J.V.,van Noordwijk, M., Silveira, E.A., Susilo, F-X., Vosti, S.A. & Nunes, P.C. (2013)  Plant functional types and traits as biodiversity indicators for tropical forests: two biogeographically separated case studies including birds, mammals and termites. Biodiversity and Conservation. 22, 1909-1930.

I am happy to respond to any clarifications.