We are searching data for your request:
Upon completion, a link will appear to access the found materials.
I'm looking for a downloadable list of all known (or better said, online documented) species in this straightforward format, as an example the European Frog:
Species: Rana temporaria
I'd like to have this list offline in a structured text or database format that I can parse. If such a list has other useful attributes (credits, distribution, common names), it is welcome, but the above is the absolute minimum I need. I know there are more taxonomy levels in the above system (Species 2000 & ITIS Catalogue of Life: April 2013 ), but I only need these basic 6.
I have been looking at several collections and am having difficulty getting the data that I need. Either the database is incomplete, not accessible as a database, has complicated data structures, or has poorly described and slow web APIs that I cannot rely on.
Conceptually, it seems to me that http://www.catalogueoflife.org comes closest to my needs, yet their download is a tool, not a database. I do see the download has a MySQL folder containing lots of files, but I don't know how to reconstruct it into a database. It seems also that they pulled the page to describe the database download.
As simple as my question seems (I'm not a biologist, so I assumed it was simple), I have wasted several hours coming up empty. I was wondering if anybody has done the work to provide basic species info in an understandable format as requested?
As for species completeness, the 1.3m of Catalogue of Life sounds really good, as I'm currently basing my system on Wikipedia, which only has 180k species.
To expand on the answer from @Rodrigo, the Integrated Taxonomic Information System seems to be a reasonable answer. It gives you a database of every taxonomic node in the Tree of Life™ and each node has a Taxonomic Serial Number (TSN). You can download the data as a database or even just use the tables as pipe-delimited text files.
For example the file
vernacularstells us that the TSN for European frog is 173444. By looking in the file
longnames, we can see that the complete name for 173444 is Rana temporaria. Finally, the file
hierarchy, tells us that the complete hierarchy for 173444 is:
→ Rana temporaria
You may download the ITIS data in several different formats from https://www.itis.gov/downloads.
Example data from some of the files.
If you downloaded the MySQL Tables data from https://www.itis.gov/downloads/itisMySQLTables.tar.gz, here are some of the useful files you'll find.
The first two fields of
vernacularscontain the TSN (Taxonomic Serial Number) and the common name for a node. Some common names map to a single TSN and not all TSNs have common names. Some examples:
50|bacteria|English|N|2015-03-02|159942 14092|mushrooms|English|N|2004-01-28|11529 14092|pore fungi|English|N|2004-01-28|11534 14092|rusts|English|N|2004-01-28|11539 183798|Domestic Cat|English|N|2007-08-15|111781
You can read the file
dropcreateloaditis.sqlto see what the other columns mean.
longnamescontains only two fields, the TSN and the complete "scientific" name of the item. For example:
50|Bacteria 14092|Basidiomycotina 183798|Felis catus
The first field of the file
hierarchyis the entire hierarchy, from tip to tail, for the TSN in the second field represented as a sequence of TSNs separated by a hyphen (
50|50|0|0|14789 555705-936287-623881|623881|936287|2|415 202423-914154-914156-158852-331030-914179-914181-179913-179916-179925-180539-552304-180580-552363-180586-183798|183798|180586|15|0
Of course, those TSNs can be looked up in the
longnamestable to convert to something human readable. Using that, here is what the first field of the last line above actually says,
Animalia → Bilateria → Deuterostomia → Chordata → Vertebrata → Gnathostomata → Tetrapoda → Mammalia → Theria → Eutheria → Carnivora → Feliformia → Felidae → Felinae → Felis → Felis catus
synonym_linksfile contains a list of obsolete TSNs and the current TSN which should replace them. For example, the TSN for the vernacular mushrooms is given as 14092 (Basidiomycotina). However, that TSN is not in the
hierarchyfile. Instead, synonym_links points us to use 623881 (Basidiomycota), which works. Here are some synonym entries:
51|50|2015-03-02 14092|623881|2004-01-28 552455|180586|2007-08-15
If you have access to a UNIX machine (MacOS may work), you can look up any common name by using a simple script I wrote. It will print a taxonomy, just like for European frog above. You can cut and paste the following commands into your terminal to try it out.
① Download the data
wget https://www.itis.gov/downloads/itisMySQLTables.tar.gz tar -axvf itisMySQLTables.tar.gz cd itisMySQL*/
② Download my lookup.py script
wget https://tinyurl.com/yyld2mm4 -O lookup.py chmod +x lookup.py
③ Run the script giving it a common name
./lookup.py human ./lookup.py domestic cat ./lookup.py love-lies-bleeding
④ Sample output
human: → Animalia → Bilateria → Deuterostomia → Chordata → Vertebrata → Gnathostomata → Tetrapoda → Mammalia → Theria → Eutheria → Primates → Haplorrhini → Simiiformes → Hominoidea → Hominidae → Homininae → Homo → Homo sapiens
Have you tried NCBI? Try this link:
I suspect you will struggle to find what you are looking for. However, you could break down your search criteria into smaller chunks to come up with some more successful (but still incomplete) results. For example, species of what? Do you really want ALL species (e.g. Bacteria, Archaea, Eukaryota)? Do you want just species that are currently alive (extant) or all species that are know to have existed at some point? Do you want sub-species?
Once you have decided on such things, you may be better off searching for individual country databases. If you do decide you want ALL species, I suggest you break down each search into smaller chunks - such as 'mammalia'.
try this one as well:
the document with the taxonomy is the taxa.txt document
Have you tried ITIS?
I once used their database. It was in MS Access format.
EDIT: Now they updated their site, and you may download PostgreSQL, MySQL, SQLite, among other formats: https://www.itis.gov/downloads/
Biology Notes on Microbial Diversity | Microbiology
The below mentioned article provides notes on microbial diversity.
The term ‘microbial diversity’ or biodiversity has become so well known that a public servant is also aware about it. Microbial diversity is defined as the variability among living organisms. The main key of microbial diversity on earth is due to evolution. The structural and functional diversity of any cell represents its evolutionary event which occurred through Darwinian Theory of natural selection.
Natural selection and survival of fittest theory is involved on the microorganisms. This includes diversity within species, between species and of ecosystems. This was first used in the title of a scientific meeting in Washington, D.C. in 1986.
The current list of the world’s biodiversity is quite incomplete (Table 2.1) and that of viruses, microorganisms, and invertebrates is especially deficient. The fungal diversity indicates the total number of species in a particular taxonomic group. The estimates of 1.5 million fungal species is based principally on a ratio of vascular plants of fungi to about 1:6 (Fig. 2.1).
Fig. 2.1 : The number of known species of microorganisms in the world.
Attempts to estimate total numbers of bacteria, archaea, and viruses even more problematical because of difficulties such as detection and recovery from the environment, incomplete knowledge of obligate microbial associations e.g. incomplete knowledge of Symbiobacterium thermophilum, and the problem of species concept in these groups.
Take the case of mycoplasmas, which are prokaryotes having obligate associations with eukaryotic organisms, frequently have tradi­tional nutritional requirements or are mono-culturable and appear to have remarkable diversity. On the other hand, there is one group Spiro plasma, which was discovered in 1972, may be the largest genus on earth.
Spiro plasma species are prin­cipally associated with insects, and the overall rate of new species isolation from such sources of 6% annually indicates species richness. Similarly, marine ecosystems likely support a luxuriant microbial diversity. Further, microbial diversity can be seen on cell size, morphology, metabolism, motility, cell division, developmental biology, adaptation to extreme conditions, etc.
The microbial diversity, therefore, appears in large measure to reflect obligate or facultative associations with higher organisms and to be determined by the spatiotemporal diversity of their hosts or associates.
1. Revealing Microbial Diversity:
The perception of microbial diversity is being radically altered by DNA techniques such as DNA-DNA hy­bridization, nucleic acid fingerprinting and methods of assessing the outcome of DNA probing, and perhaps most important at present, is 16S rRNA sequencing.
The 16S rRNA has radically changed the classification of microbes into 3 domains, the Bacteria, Archaea and Eukarya. While DNA-based analysis (DNA fingerprinting by restriction fragment length polymor­phism i.e. RFLP analysis) is another accepted technique for evaluation of re­lationships between organisms, especially if they are closely related. Holben (1988) detected Brady-rhizobium japonicum selectively at densities as low as 4.3 х 10 3 organisms/gram dry soils.
2. The Concept of Microbial Species:
Biological diversity or biodiversity is actually evolved as part of the evolution of organisms, and the smallest unit of microbial diversity is a species. Bacteria, due to lack of sexuality, fossil records etc., are defined as a group of similar strains distinguished sufficiently from other similar groups of strains by genotypic, phenotypic, and ecological characteristics.
The adhoc committee on (he reconciliation of approach to international committee on systematic bacteriology (ICSB) recommended in 1987 that bacterial species would include strains with approximately 70% or more DNA-DNA relatedness and with 5% or less in thermal stability.
Hence, a bacterial species is a genomic species based on DNA-DNA relatedness and the modern concept of bacterial species differs from those of other organisms. To date, more than 69,000 species in 5100 genera of fungi and about 4,760 species of about 700 genera of bacteria have been described in the literature as given in Table 2.1.
3. Significance of Study of Microbial Diversity:
As quoted by American Society of Microbiology under Microbial Diversity Research Priority, “microbial diversity encompasses the spectrum of variability among all types of microorganisms in the natural world and as altered by human intervention”. The role of microorganisms both on land and water, including being the first colonizer, have ameliorating effects of naturally occurring and man-made disturbed environments.
Current evidence suggests there exist perhaps 3 lakh to 10 lakh species of prokaryotes on earth but only 3100 bacteria are described in Bergey’s Manual. More and more information’s are required and will be of value because microorganisms are important sources of knowledge about strategies and limits of life.
There are resources for new genes and organisms of value to biotechnology, there diversity patterns can be used for monitoring and predicting environmental change. Microorganisms play role in conservation and restoration biology of higher organisms. The microbial communities are excellent model for understanding biological interactions and evolutionary history.
Molecular microbiological methods involving DNA-DNA hybridization and 16S rRNA sequencing, etc. now more helpful in establishing microbial diversity. Data bases are becoming more widely available as a source of molecular and macromolecular information on microorganisms. New- technologies are being developed that are based on diverse organisms from diagnostics to biosensors and to biocatalysts.
In the year 1990s’ microbial diversity has burst forward in a new and exciting form due to efforts of environmental microbiologists, who kept the diversity flame alive during the paradigm organism years.
The molecular revolution that has been sweeping through environmental microbiol­ogy has shown how diverse microbes really are. It has also leashed new waves of creativity in the from of RNA sequence analysis to prove the metabolic activities and gene regulation of microbes in situ.
The gainful advantages may occur by enriching microbial diversity. Microbial genomes can be used for recombinant DNA technology and genetic engineering of organisms with environmental and energy related applications. Emergence of new human pathogen such as SARS is becoming quite important due to threat to public health can be solved by analyzing the genomes of such pathogen.
Culture collections can play a vital role in preserving the genetic diversity of microorganisms. Microbial information’s including molecular, phenotypic, chemical, taxonomic, metabolic, and ecological information can be deposited on databases. A large number of yet unexplored microorganisms may lead to beneficial information’s.
This can be further strengthened by multidisciplinary involvement of experts. There is a compelling need for discovery and identification of microbial bio-control agents, an assessment of their efficacy etc.
The mo­lecular nature of genomes of some important pathogens is necessary to understand the pathogenesis, bio-control, and bioremediation of pollution etc., besides helping in rapid de­tection and diagnosis and in identification of genes for transfer of desirable properties.
Microorganisms are sensitive indicators of envi­ronmental quality. Thus, microbial diversity may be helpful in determining the environmen­tal state of a given habitat of ecosystem. The diverse microorganisms can cause disease and could potentially be used as biological weap­ons. Knowing what is likely to be present can help in rapid diagnosis and treatment.
Biodegradation and bioremediation are potentially important to clean-up and destruction of unwanted materials. Microbial diversity of marine microorganisms is equally important. Sometimes, it is helpful to solve the contamination of sea­food by pathogenic microorganisms e.g. Vibrio vulnificus contaminated oysters. Blue green algae and cyanophages are another dangerous organisms to aquaculture industries.
4. Microbial Evolution:
The microbial evolution has entered a new era with the use of molecular phylogenies to determine relatedness. Certainly this type of phylogenetic analysis remains controversial, but it has opened up possibility of comparing very diverse microbes with a single yardstick and attempting to deduce their history.
Some scientists have opined that the ‘failure’ of molecular methods of find a single unambiguous evolutionary progression from a single ancestor to the present panoply of microorganisms.
The increasing appreciation of the ubiquity and frequency of gene transfer events open the possibility of learning quite essential prokaryotes is by establishing a central core of genes that has not participated in the general orgy of gene transfer. The increasing number of genome sequences may also contribute to a better understanding of the evolutionary history of microbe.
The evolution of life on Earth over the past 4 billion years has resulted in a huge variety of species. For more than 2,000 years, humans have been trying to classify the great diversity of life. The science of classifying organisms is called taxonomy. Classification is an important step in understanding the present diversity and past evolutionary history of life on Earth.
All modern classification systems have their roots in the Linnaean classification system. It was developed by Swedish botanist Carolus Linnaeus in the 1700s. He tried to classify all living things that were known at his time. He grouped together organisms that shared obvious physical traits, such as number of legs or shape of leaves. For his contribution, Linnaeus is known as the &ldquofather of taxonomy.&rdquo You can learn more about Linnaeus and his system of classification by watching the video at this link: http://teachertube.com/viewVideo.php?video_id=169889.
The Linnaean system of classification consists of a hierarchy of groupings, called taxa(singular, taxon). Taxa range from the kingdom to the species (see Figure below). The kingdom is the largest and most inclusive grouping. It consists of organisms that share just a few basic similarities. Examples are the plant and animal kingdoms. The species is the smallest and most exclusive grouping. It consists of organisms that are similar enough to produce fertile offspring together. Closely related species are grouped together in a genus.
Linnaean Classification System: Classification of the Human Species. This chart shows the taxa of the Linnaean classification system. Each taxon is a subdivision of the taxon below it in the chart. For example, a species is a subdivision of a genus. The classification of humans is given in the chart as an example.
Perhaps the single greatest contribution Linnaeus made to science was his method of naming species. This method, called binomial nomenclature, gives each species a unique, two-word Latin name consisting of the genus name and the species name. An example is Homo sapiens, the two-word Latin name for humans. It literally means &ldquowise human.&rdquo This is a reference to our big brains.
Why is having two names so important? It is similar to people having a first and a last name. You may know several people with the first name Michael, but adding Michael&rsquos last name usually pins down exactly whom you mean. In the same way, having two names uniquely identifies a species.
Revisions in Linnaean Classification
Linnaeus published his classification system in the 1700s. Since then, many new species have been discovered. The biochemistry of many organisms has also become known. Eventually, scientists realized that Linnaeus&rsquos system of classification needed revision.
A major change to the Linnaean system was the addition of a new taxon called the domain. Adomain is a taxon that is larger and more inclusive than the kingdom. Most biologists agree there are three domains of life on Earth: Bacteria, Archaea, and Eukaryota (see Figure below). Both Bacteria and Archaea consist of single-celled prokaryotes. Eukaryota consists of all eukaryotes, from single-celled protists to humans. This domain includes the Animalia (animals), Plantae (plants), Fungi (fungi), and Protista (protists) kingdoms.
This phylogenetic tree is based on comparisons of ribosomal RNA base sequences among living organisms. The tree divides all organisms into three domains: Bacteria, Archaea, and Eukarya. Humans and other animals belong to the Eukarya domain. From this tree, organisms that make up the domain Eukarya appear to have shared a more recent common ancestor with Archaea than Bacteria.
Examples of Taxonomy
The scientific classification of humans is as follows:
- Domain: Eukaryota
- Kingdom: Animalia
- Phylum: Chordata
- Class: Mammalia
- Order: Primates
- Family: Hominidae
- Genus: Homo
Another example of taxonomy is the diagram below, which shows the classification of the red fox, Vulpes vulpes (sometimes the genus and species names are the same, even though these are two different ranks).
Many mnemonic devices can be used to remember the order of the taxonomic hierarchy, such as “Dear King Philip Came Over For Good Spaghetti”.
(1). Telocentric chromosome
Ø In telocentric chromosomes, the centromere is located at the proximal end (tip) of the chromosome.
Ø The chromosomal tips are called as telomeres.
Ø Thus, telocentric chromosomes are long rod-like chromosomes
Ø These chromosomes appear as ‘i’ shaped structure in the metaphase stage of cell cycle.
Ø This type of chromosome has only one chromosomal arm.
Ø Telocentric chromosomes are very rare in occurrence and they were reported only in very few species.
Ø The centromere is positioned at one end of the chromosome in such a way that it produces a very short arm (p) and an exceptionally long arm (q).
Ø Acrocentric chromosomes appear as ‘J’ shaped structures in the metaphase stage of the cell cycle.
Ø The group Acrididae (grasshoppers) shows this type of chromosomes.
Ø The name is derived from the Acrididae (family of grasshoppers).
Ø All acrocentric chromosomes will be sat-chromosomes.
Ø Sat-chromosome = a chromosome with a secondary constriction and a knob-like structure at one end.
Ø In human, the chromosome number 13, 15, 21 and 22 are sat-acrocentric chromosomes.
Ø The centromere is located near the centre of the chromosome (NOT in the exact centre).
Ø Thus, these chromosomes will have two unequal arms a small ‘p’ – arm and a large ‘q’ – arm.
Ø Sub-metacentric chromosomes appear as ‘L’ shaped structures in the metaphase stage of cell division.
Ø Majority of the human chromosomes are sub-metacentric chromosomes.
Ø The centromere is located exactly at the centre of the chromosome.
Ø Thus, these chromosomes will have two equal sized arms.
Ø The metacentric chromosomes will appear as ‘V’ shaped structures in the metaphase stage of cell division.
Ø Metacentric chromosomes are considered as a primitive type of chromosome.
Ø Primitive organism shows a karyotype with a majority of the chromosomes in metacentric shapes.
The scientific order Primates encompasses about 233 living species classified in 13 scientific families. Most primates live in tropical forests and vary greatly in size. The smallest primate member is the pygmy mouse lemur (Microcebus myoxinus) weighing around 31 g (1.1 oz.) and the gorilla is the largest primate weighing up to 220 kg (484 lbs.).
Family - Hominidae
Historically humans and their extinct ancestors were classified in the Family Hominidae while all great apes (chimpanzees, bonobos, gorillas, and orangutans) were classified in the Family Pongidae. However, biomolecular and genetic research along with recent fossil evidence have identified new similarities between species, leading to the reclassification of chimpanzees and gorillas into the Family.
Genus, Species - Gorilla & beringei
In the past, gorilla scientific classification had one species (gorilla) that was divided into three subspecies. Each of these subspecies was distinguished from one another by their geographic location in Africa.
- Western lowland gorilla (Gorilla gorilla gorilla) is the smallest of all three subspecies &mdash weighing around 180 kg (396 lbs.) for an adult male &mdash and lives in the tropical forests of West Africa. Lowland gorillas in general are similar in appearance. The western lowland gorilla is the most common type of gorilla found in zoological facilities and is the species cared for at Busch Gardens Tampa Bay.
- Eastern lowland gorilla (Gorilla gorilla graueri) is slightly larger in size weighing up to 220 kg (484 lbs.) and darker in coloration than the western lowland gorilla. They live in the rainforests of central Africa.
- Mountain gorilla (Gorilla gorilla beringei) is the largest and rarest of all three subspecies. Adult males may weigh over 227 kg (500 lbs.) They are found at high elevations of the Virunga Volcano range that separates Democratic Republic of the Congo from Rwanda and Uganda. Their hair is longer and darker than their lowland counterparts due to the colder climate of the high elevation. Mountain gorillas are taller, have a more pointed head, have a wider gap in the middle of the nose, and lack a reddish patch of hair on their heads, common to lowland gorillas.
In 2001 mitochondrial DNA research and morphological variances have led to the scientific reclassification of gorillas. Under the new classification gorillas are divided into two species, the eastern gorilla (Gorilla beringei) and the western gorilla (Gorilla gorilla). It is thought that the two species diverged from one another about 2 million years ago and both have two subspecies.
- The eastern gorilla's two subspecies are the eastern lowland gorilla (Gorilla beringei graueri) and the mountain gorilla (Gorilla beringei beringi).
- It has been suggested that there is a third subspecies of eastern gorillas because a small subset of mountain gorillas that inhabit the Bwindi National Park in Uganda possess distinctive characteristics such as morphology, ecology and behavior. Due to the small size of mountain gorilla populations and available samples for testing, it is difficult to determine whether the two populations are physically and genetically distinct enough to be considered two separate subspecies.
- The western gorilla's two subspecies are the western lowland gorilla (Gorilla gorilla gorilla) and the Cross River gorilla (Gorilla gorilla diehli).
The name "gorilla" was derived from an ancient account by a Carthaginian explorer who sailed along the west coast of Africa nearly 2,500 years ago. Local people shared their name for the great ape with him &mdash the rough translation of which meant "hairy person".
Mountain gorillas live around the Virunga Mountain Range. Virunga translated means "a lonely mountain that reaches the clouds".
Primates may be divided into two suborder groups.
- Prosimii (prosimians)
- Prosimians are said to be primitive because some of their physical characteristics are found in other mammals but are generally not shared in other primates. For example prosimians have a nose structure that remains moist, called a rhinarium (also found in dogs), that enhances their sense of smell.
- Anthropoids are further divided into New World & Old World anthropoids. New World anthropoids are native to North & South America whereas Old World anthropoids are native to Africa & Asia.
- Apes are further divided into greater & lesser ape categories. Lesser apes include the 11 recognized species of gibbons and siamangs native to Southeast Asia. Greater apes are native to both Africa and Asia, and include orangutans, chimpanzees, bonobos and gorillas.
Apes diverged from Old World monkeys about 25 million years ago. There are many differences between apes and monkeys, including the following characteristics:
- Apes have no tail
- Apes usually have a larger body size & weight
- Apes have more of an upright body posture
- Apes have broader chests
- Apes rely more on vision than on smell (have a short broad nose rather than a long snout)
- Apes have longer gestations and need longer periods of time to mature.
- Great apes tend to be less arboreal (tree-dwelling) and more terrestrial (ground-dwelling). This has led to many changes in the muscle and skeletal structure of their arms because they are not as adapted for tree-dwelling (brachiation - swinging from trees) as monkeys are.The fossil record indicates that lesser and greater apes diverged from one another about 18 million years ago. The Pongidae family (orangutans) diverged about 14 million years ago, gorillas about 7 million years ago, and chimpanzees and humans diverged about 6 million years ago.
- Humans have about 98.4% of our DNA (deoxyribonucleic acid - genetic material) in common with chimpanzees. This genetic information has provided insight to human-relatedness to other great apes such as the gorilla. Humans are more closely related to chimpanzees and gorillas than either of them are to orangutans.
Discovery of the Modern Gorilla
According to the fossil record, ape descendants originated in Africa more than 25 million years ago and then dispersed throughout Asia and Europe.
Over 15 genera of apes have been identified by paleontologists to have lived during the Miocene Era (23 million years ago) in places such as Italy and Greece.
Nearly 2,500 years ago an expedition from the Phoenician merchant city of Carthage to western coasts of Africa accidentally discovered a group of wild gorillas.
During the sixteenth century an English sailor by the name of Andrew Battel was captured by the Portuguese in West Africa. He spoke of two man-like apes (today easily recognized as chimpanzees & gorillas) that would visit the campfire when it was unattended.
The mountain gorilla was first discovered by a German officer, named Captain Robert von Beringe in 1902. Prior to this time, only lowland gorillas were known to exist. The mountain gorilla subspecies name is derived from Captain Robert von Beringe's last name (Gorilla beringei beringei).
Evolutionary Perspectives of the Gorilla
Many ancient explorers and African tribes have described gorillas as primitive hairy people. They have also been referred to as anthropoid or "man-like" apes.
During the 1600s very little was known about apes and scientific literature often confused the greater apes with pygmy tribesmen.
In 1860 an explorer named Du Chaillu described the gorilla as a bloodthirsty forest monster that is willing to attack any human beings. Author Alfred Brehm discounted Du Chaillu's claim in the 1876 book, Thierleben (Animal Life).
The gorilla's intimidating appearance, extreme strength, and chest-beating displays have given them an unfortunate and inaccurate ferocious stereotype. Several mainstream movies have perpetuated this false stereotype, resulting in misconceptions as to gorillas' true gentle nature.
The first documented gorilla research was in 1959 by George Schaller. His book was entitled The Year of the Gorilla. This was one of the first books that dispelled many myths such as the savage nature of gorillas.
In 1963, Dian Fossey began her study, research and conservation of mountain gorillas. In 1983, she published a book entitled Gorillas In The Mist. In 1986, a movie based on her book brought gorilla conservation to worldwide attention.
Nematode Parasites of Domestic Animals
Animal Group Nematode Species Rodents Angiostrongylus cantonensis Nippostrongylus brasiliensis Syphacia obvelata Capillaria hepatica Cattle Dictyocaulus viviparus Oesophagostomum radiatum Onchocerca gutterosa Horses Strongylus edentatus Parascaris equorum Oxyuris equi Pigs Stephanurus dentatus Ascaris suum Sheep Haemonchus contortus Ostertagia ostertagi Dogs Driofillaria spp. Dioctophyma renale Chickens Syngamus trachea Ascaridia galli Heterakis gallinarum
External Earthworm Anatomy
What is the external anatomy of an earthworm?
The external body of an earthworm is well adapted for living in the soil, similar to the external structure of other insects. The front or head of the worm is called the anterior. The very first section of the anterior contains the mouth and prostomium. The prostomium is a kind of lip which is located on the front of the mouth. Earthworms lose moisture and breathe via their skin. They have light-sensitive cells across their external structure, which are scattered around the skin. These cells give earthworms the ability to detect changes in lighting, and these cells are also sensitive to chemicals and touch. The body is separated in segments which resemble rings. Each segment has a number of bristly hairs attached to it, which helps the earthworm to move around. On mature earthworms, you will find a saddle or glandular ring called a clitellum. When an earthworm has mated, the clitellum will secrete a sack of eggs. The final segment of an earthworm contains the anus which is where waste is secreted.
1. Put on safety goggles, gloves, and a lab apron.
2. Place earthworm in the dissecting tray & rinse off the excess preservative. Identify the dorsal side, which is the worm’s rounded top, and the ventral side, which is its flattened bottom. Turn the worm ventral side up, as shown in the earthworm anatomy diagram below.
3. Use a hand lens as you observe all parts of the worm, externally and internally. Locate the conspicuous clitellum, a saddle-like swelling on the dorsal surface. The clitellum produces a mucus sheath used to surround the worms during mating and is responsible for making the cocoon within which fertilized eggs are deposited. The anterior of the animal is more cylindrical than the flattened posterior and is the closest to the clitellum. The ventral surface of the earthworm is usually a lighter colour than the dorsal surface. The mouth is located on the ventral surface of the first segment while the anus is found at the end of the last segment. Find the anterior end by locating the prostomium (lip), which is a fleshy lobe that extends over the mouth. The other end of the worm’s body is the posterior end, where the anus is located.
4. Locate the clitellum (the reproductive organ), which extends from segment 33 to segment 37. Look for the worm’s setae, which are the minute bristle-like spines located on every segment except the first and last one. Run your fingers over the ventral surface of the earthworm’s body. You should be able to feel bristle-like setae used for locomotion
5. Refer again to the diagram of the ventral view of the worm to locate and identify the external parts of its reproductive system. Find the pair of sperm grooves that extend from the clitellum to about segment 15, where one pair of male genital pores is located. Look also for one pair of female genital pores on segment 14. There is another pair of male genital pores on about segment 26. Try to find the two pairs of openings of the seminal receptacles on segment 10. Note: These openings are not easy to see.
A classification of living organisms
Recent advances in biochemical and electron microscopic techniques, as well as in testing that investigates the genetic relatedness among species, have redefined previously established taxonomic relationships and have fortified support for a five-kingdom classification of living organisms. This alternative scheme is presented below and is used in the major biological articles. In it, the prokaryotic Monera continue to comprise the bacteria, although techniques in genetic homology have defined a new group of bacteria, the Archaebacteria, that some biologists believe may be as different from bacteria as bacteria are from other eukaryotic organisms. The eukaryotic kingdoms now include the Plantae, Animalia, Protista, and Fungi, or Mycota.
The protists are predominantly unicellular, microscopic, nonvascular organisms that do not generally form tissues. Exhibiting all modes of nutrition, protists are frequently motile organisms, primarily using flagella, cilia, or pseudopodia. The fungi, also nonvascular organisms, exhibit an osmotrophic type of heterotrophic nutrition. Although the mycelium may be complex, they also exhibit only simple tissue differentiation, if any at all. Their cell walls usually contain chitin, and they commonly release spores during reproduction. The plants are multicellular, multitissued, autotrophic organisms with cellulose-containing cell walls. The vascular plants possess roots, stems, leaves, and complex reproductive organs. Their life cycle shows an alternation of generations between haploid (gametophyte) and diploid (sporophyte) generations. The animals are multicellular, multitissued, heterotrophic organisms whose cells are not surrounded by cell walls. Animals generally are independently motile, which has led to the development of organ and tissue systems. The monerans, the only prokaryotic kingdom in this classification scheme, is principally made up of the bacteria. They are generally free-living unicellular organisms that reproduce by fission. Their genetic material is concentrated in a non-membrane-bound nuclear area. Motility in bacteria is by a flagellar structure that is different from the eukaryotic flagellum. Most bacteria have an envelope that contains a unique cell wall, peptidoglycan, the chemical nature of which imparts a special staining property that is taxonomically significant (i.e., gram-positive, gram-negative, acid-fast).
The use of “division” by botanists and “phylum” by zoologists for equivalent categories leads to a rather awkward situation in the Protista, a group of interest to both botanists and zoologists. As used below, the terms follow prevailing usage: phylum for the primarily animal-like protozoa and division for other protistan groups that are more plantlike and of interest primarily to botanists.
The discussion above shows the difficulty involved in classification. For example, one traditional classification of the Aschelminthes, presented below and in the article aschelminth, divides the phylum Aschelminthes into five classes: Rotifera, Gastrotricha, Kinorhyncha, Nematoda, and Nematomorpha. An alternative classification elevates these classes to phyla, and still another classification establishes different relationships between the groups—phylum Gastrotricha, phylum Rotifera, phylum Nematoda (containing classes Adenophorea, Secernentea, and Nematomorpha), and phylum Introverta (containing classes Kinorhyncha, Loricifera, Priapulida, and Acanthocephala). The true relationships between these pseudocoelomates remain to be established.
I thank J. Wiens for organizing the 2006 SSB symposium on species delimitation and for inviting me to contribute this paper. L. Knowles provided valuable information about methods based on coalescent theory, and J. Sites, J. Wiens, and an anonymous reviewer provided comments on an earlier version. I have previously acknowledged the contributions of numerous colleagues to the development of my views on species concepts (see de Queiroz, 1998, 1999, 2005a, 2005b, 2005c).