Biological Diversity [BIOLOGY]

• Taxonomy & Binomial Nomenclature

  The branch of biology concerned with identifying, naming, and classifying organisms is called Taxonomy. The basis of taxonomy is a system introduced by naturalist Carolus Linnaeus, who devised a means of naming organisms and a hierarchical scheme of classifying these organisms into groups within broader groups. As such, Linnaeus’ system of naming organisms is the standard for naming organisms and is called a “scientific name”.
• Taxonomy & Binomial Nomenclature

  In his naming system, an organism is assigned a two-part name. Hence, this system is referred to as the binomial nomenclature system. The first part of the scientific name is the genus (plural, genera) which is a larger group. This is then followed by the species name (or specific epithet in the more technical use of the term) of the organism. Cases LIKE milkfish, the bangus, which has Chanos chanos for its scientific name.called tautonymy and may signify that the species is representative of the characteristics of the genus.
• Hierarchies of Classification

  • Life
  • Domain
  • Kingdom
  • Phylum
  • Class
  • Order
  • Family
  • Genus
  • Species
• Prokaryota

  • Bacteria
  • Archaea

  Eukaryota

  • Protista
  • Plantae
  • Fungi
  • Animalia
• The Prokaryotic Domains

  • Spherical cells are called cocci (singular coccus)and when they appear as chains, they are called streptococci. Others may appear as clusters and are referred to as staphylococci.
  • Rod-shaped prokaryotes are called bacilli (singular bacillus). Bacilli may also be threadlike or filamentous.
  • The third is spiral prokaryotes. Short and rigid prokaryotes are called spirilla while longer cells are called spirochetes.
• The Prokaryotic Domains

  • Domain Archaea

  Members of this domain thrive in many habitats, including places where few other organisms survive. This is because they have molecular features that enable them to survive such extreme conditions.
• The Prokaryotic Domains

  • Domain Archaea
  • Extreme Halophiles or “Salt Lovers” thrive in conditions where the salt concentration is extremely high. Remember, osmoregulation is an important feature of life, and so archaea must take extreme measures with regards to this.
  • Extreme Thermophiles or “Heat Lovers” thrive in areas with high temperatures. They can also be present in areas of high acidity.
  • Methanogens are archaea that thrive in oxygen-lacking environments and, as the name suggests, live on other gases in the area such as methane.
• The Prokaryotic Domains

  • Domain Bacteria

  Bacteria, microscope work on them began earlier and had allowed us to view them through staining methods. In this regard, bacteria can be stained as Gram-negative or Gram-positive.
• The Prokaryotic Domains

  • Domain Bacteria

  The domain is divided into five groups based on their genetic differences:

  • Proteobacteria are Gram-negative bacteria and share a common rRNA sequence. Examples include pathogenic bacteria such as Vibrio cholerae that causes cholera and those that are residents of the body like Escherichia coli (E. coli).
  • Gram-positive bacteria rival the proteobacteria in terms of diversity. Soil-dwelling Streptomyces are cultured by pharmaceutical companies to create antibiotics (Streptomycin). There are also pathogens in this group.
• The Prokaryotic Domains

  • Domain Bacteria
  • The cyanobacteria are the only ones that are plant-like and are able to photosynthesize. It is believed that the origins of chloroplasts in plants are linked to cyanobacteria.
  • Chlamydias are parasites of eukaryotic hosts. Chlamydia is one of the most common sexually transmitted infections because of this group.
  • Spirochetes are helical bacteria that rotate to move through their environment. Some spirochetes are notorious for causing syphilis (Treponema pallidum) and Lyme disease (Borrelia burgdorferi).
• The Eukaryotic Domains

  • Protists

  Protist is the term used on these unicellular eukaryotes. They once belonged to their Kingdom, Protista, but due to their extreme diversity, it is difficult to categorize these organisms into a specific group. Hence, protists are conveniently referred to as eukaryotes that are not plants, animals, or fungi. One of the groupings is for protists that are plant-like and can photosynthesize: the algae. Others are heterotrophs and parasitic in nature; these protists are informally called protozoans. Still, other protists can be both
• The Eukaryotic Domains

  • Protists
  • Diatoms and Algae – photosynthetic protists.
  • Dinoflagellates – common components of marine and freshwater plankton (organisms that drift in aquatic environments). Some cause red tides but there are also beneficial ones like those that provide food for corals.
  • Ciliates – have cilia to move and sweep food into their mouth. This includes Paramecium.
  • Amoebas – move and feed by means of pseudopodia, temporary extensions of the cell
• The Eukaryotic Domains

  • Fungi

  All fungi are heterotrophs and nourish themselves through absorption. They secrete powerful enzymes that are able to break macromolecules into monomers and absorb the broken-down nutrient molecules into their cells
• The Eukaryotic Domains

  • Fungi

  Because they secrete powerful enzymes, most feed on decaying matter, and fungi are essential decomposers in most ecosystems. However, not all fungi are decomposers. Some form a beneficial relationship with other organisms, termed symbiosis, an example of which is the mycorrhiza (plural mycorrhizae) where the fungi associate itself with plant roots. Other fungi form symbiotic relationships with green algae or cyanobacteria forming lichens.
• The Eukaryotic Domains

  • Fungi

  The feeding structures of fungi are composed of threadlike filaments called hyphae. These hyphae branch repeatedly as they grow, forming a mass called mycelium (plural mycelia). Since fungi are immobile, the mycelium acts like hands that extend, without enlarging, at a phenomenal rate to scour for food. This allows the fungi to cover more area and since the mycelium does not enlarge, more surface area can be utilized for absorption
• The Eukaryotic Domains

  • Fungi

  The umbrella-like structure that we recognize as fungi are reproductive structures made of tightly packed hyphae. The hyphae are surrounded by a cell wall composed of chitin, the same as those found in external skeletons of insects.
• The Eukaryotic Domains

  • Fungi

  Spores can be produced sexually or asexually. Those that solely rely on spore production asexually are called imperfect fungi and these include the molds and yeasts, the latter pertaining to a single-celled fungus that reproduces by budding or pinching small buds from the original parent cell.
• The Eukaryotic Domains

  • Fungi

  There are different groups of fungi but the one we are most familiar with falls into the club fungi group. Technically called basidiomycetes because of the club-shaped, spore-producing structure called a basidium. Many basidiomycete species specialize in breaking down lignin, which is found in wood and thus plays a key role as decomposers.
• The Eukaryotic Domains

  • Plants

  The first are plants that are seedless and nonvascular, that is to say, they do not have vascular systems composed of the xylem and phloem (more on this in Plant Forms and Functions). These include plants such as mosses, liverworts, and hornworts. Collectively, they are called bryophytes (Phylum Bryophyta). Bryophytes lack true roots and leaves.
• The Eukaryotic Domains

  • Plants

  Then there are vascular plants. The first vascular plants are seedless. These seedless vascular plants are composed of two phyla: the lycophytes (which include club mosses, spike mosses, and quillworts) and the monilophytes (the ferns, horsetails, and whisk ferns). Later on, vascular plants with seeds appeared. A seed contains the plant’s embryo packed with food supply and with a protected covering.
• The Eukaryotic Domains

  • Plants

  Seed plants are classified into non-flowering or flowering plants. The non-flowering seed plants are called gymnosperms and they include phyla where conifers as well as the ginkgo tree, and some palm-like cycads belong to. Flowering vascular plants are called angiosperms belonging to a single phylum, the anthophytes. Flowers are complex reproductive structures that develop seeds in protective chambers
• The Eukaryotic Domains

  • Animal

  Animals are multicellular, heterotrophs (few exceptions exist) that obtain nutrients through ingestion. Animals generally fall into two categories: invertebrates and vertebrates, referring to the lack or presence of a backbone respectively. The large majority of animals are invertebrates while we humans belong to the vertebrates. Animals can be characterized by basic features of the body called “body plan”.
• The Eukaryotic Domains

  • Animal

  One feature of a body plan is symmetry. Two types of symmetry are present in animals: radial symmetry and bilateral symmetry. Radially symmetric animals have body parts that radiate from a center; imagine how a bicycle tire has a center with spokes that go to the wheel. Bilaterally symmetric animals have mirror images of left and right sides. In addition, these animals have a distinct head or anterior; tail, or posterior; a back, or dorsal side; and a bottom, or ventral, surface
• The Eukaryotic Domains

  • Animal

  The other feature is based on how the animal embryo develops in a process called gastrulation
• The Eukaryotic Domains

  • Animal

  Animals can be considered protostomes if the first opening that forms during gastrulation becomes the mouth. The other group, the deuterostomes, have this opening that becomes the anus and develops a second opening that becomes the mouth. These two features have allowed biologists to categorize the animals. We will now look into them in greater detail.
• The Eukaryotic Domains

  • Animal

  Sponges (Phylum Porifera) are considered the most basic of animals having no tissues. Animals with tissues form a bigger group called Eumetazoa. This group is split based on the symmetry of the body. Those with radial symmetry developed into the Phylum Cnidaria which includes corals and jellyfish. The other group, with bilateral symmetry called Bilateria, diversified even further into three large groups: Lophotrochozoa, Ecdysozoa, and Deuterostomia.
• The Eukaryotic Domains

  • Animal

  The first group includes many phyla such as those of flatworms, mollusks, and annelids and is based on a feeding apparatus called the lophophore in some phyla and a trochophore type of larva in mollusks and annelids
• The Eukaryotic Domains

  • Animal

  Ecdysozoans include the nematodes and arthropods. The group got its name from the process of ecdysis, where the external skeleton of the organism must be shed first before the animal could grow. Think butterflies and lobsters. The two groups usually have a protostome type of embryonic development while the last group pertains to the deuterostome type of development.
• The Eukaryotic Domains

  • Animal [Invertebrates]

  Phylum Porifera (Sponges) are the simplest animals due to having no tissues. But they have cells that sense and react to changes in the environment. The body of a sponge is composed of 2 layers: the inner layer: cells called choanocytes that help move water through the sponge’s body. The other layer: amoebocytes that produce supportive skeletal fibers called spongin or mineralized particles called spicules. The sponges used in baths are those that contain only spongin. Adult sponges are sessile in that they are anchored in place.
• The Eukaryotic Domains

  • Animal [Invertebrates]

  Phylum Cnidaria encompasses animals with radial symmetry and bodies that arise from only two layers of tissue. Cnidarians have two body forms: The first is a polyp and is exemplified by hydras and sea anemones which have a cylindrical body with tentacles projecting from one end; the other is the medusa, umbrella-shaped with a fringe of tentacles around the lower edge, as shown by the jellyfish. This phylum is named after its stinging cells called cnidocytes.
• The Eukaryotic Domains

  • Animal [Invertebrates: Lophotrochozoan Phyla]

  Phylum Platyhelminthes (Flatworms) are deuterostomes that lack a body cavity. There are three major groups of flatworms: The first are planarians, free-living flatworms; the second are the flukes, which are parasites of other animals; the last group, the tapeworms, are also parasites of other animals.
• The Eukaryotic Domains

  • Animal [Invertebrates: Lophotrochozoan Phyla]

  Phylum Mollusca includes soft-bodied animals with variations on a common body plan. A mollusk consists of three main parts: A muscular foot, for locomotion; a visceral mass containing the internal organs; and a mantle, a fold of tissue that drapes over the visceral mass. Another feature of mollusks is a unique rasping organ called a radula. The three most diverse groups under the phyla include gastropods, bivalves, and cephalopods.
• The Eukaryotic Domains

  • Animal [Invertebrates: Lophotrochozoan Phyla]

  Phylum Annelida (Segmented Worms) are characterized by segmentation (i.e., their body has begun to be divided into a series of repeated parts). An example is the earthworm and marine worms such as polychaetes. Annelids can be grouped based on their lifestyle: Errantia are mobile annelids; the others are Sedentarians which tend to be less mobile.
• The Eukaryotic Domains

  • Animal [Invertebrates: Ecdysozoan Phyla]

  Phylum Nematoda (Roundworms) have a complete digestive tract, that is to say, they have a mouth and anus for ingestion and egestion respectively. Nematodes are cylindrical and are covered in a layer called a cuticle that helps them prevent drying out. Nematodes can be free-living or parasitic.
• The Eukaryotic Domains

  • Animal [Invertebrates: Ecdysozoan Phyla]

  Phylum Arthropoda is a group composed of segmented animals with a hard exoskeleton and jointed appendages. Arthropods grow through molting or ecdysis where they shed their exoskeleton and grow a new one. The arthropods consist of groups called chelicerates, myriapods, and pancrustaceans
• The Eukaryotic Domains

  • Animal [Invertebrates: Ecdysozoan Phyla]

  Chelicerates have clawlike, feeding appendages. The horseshoe crab and arachnids (scorpions, spiders, ticks, and mites) belong in this group. Myriapods resemble annelids but have jointed legs. The millipedes and centipedes belong to this group. The anatomical distinction between the two is that the former has two pairs of short legs per body segment while the latter has one pair of legs per segment. Pancrustaceans include the crustaceans and the insects, the latter considered the most successful invertebrate.
• The Eukaryotic Domains

  • Animal [Invertebrates: Deuterostome Phyla]

  Phylum Echinodermata refers to the animals’ prickly bumps or spines as in the case of sea stars or sea urchins. These extensions of the animal’s internal skeleton are called endoskeletons. These animals are bilaterally symmetrical as larvae but develop into radially symmetric adults. Sea stars, sea urchins, sand dollars, and brittle stars belong in this group
• The Eukaryotic Domains

  • Animal [Invertebrates: Deuterostome Phyla]

  Phylum Chordata which includes us. But wait, aren’t we vertebrates? Well, the earliest chordates developed a backbone, technically the vertebra, from invertebrate ancestors. Four features identify members of the phylum: (1) a dorsal, hollow nerve cord; (2) a notochord, a rod located between the digestive tract and the nerve cord; (3) pharyngeal slits located in the pharynx; and (4) a muscular post-anal tail. The chordates which retained invertebrate features are the lancelets and the tunicates.
• The Eukaryotic Domains

  • Animal [Vertebrates]

  This structure serves as the only skeletal support for the lancelets and tunicates but the development of the vertebral column and a skull allowed the vast majority of vertebrates to enclose and protect the nerve cord while taking on a structural support function
• The Eukaryotic Domains

  • Animal [Vertebrates]

  Fish with jaws began with cartilaginous fishes, called chondrichthyans. These fish are made primarily of cartilage. This group includes sharks and rays. Ray-finned fishes such as tuna, trout, and goldfish developed skeletons made of bone. Lobe-finned fish have a series of rod-shaped bones on their muscular pectoral and pelvic fins. This group includes the coelacanth and lungfish, the latter showing a transition phase since they are able to gulp air and have lung structures.