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APPENDIX A   The Tree of Life

Phylogeny is the organizing principle of modern biological taxonomy. A guiding principle of modern phylogeny is monophyly. A monophyletic group is considered to be one that contains an ancestral lineage and all of its descendants. Any such group can be extracted from a phylogenetic tree with a single cut.

The trees shown here provide a guide to the relationships among the major groups of extant (living) organisms in the tree of life as we have presented them throughout this book. The position of the branching “splits” indicates the relative branching order of the lineages of life, but the time scale is not meant to be uniform. In addition, the groups appearing at the branch tips do not necessarily carry equal phylogenetic “weight.” For example, the ginkgo [78] is indeed at the apex of its lineage; this gymnosperm group consists of a single living species. In contrast, a phylogeny of the eudicots [86] could continue on from this point to fill many more trees the size of this one.

The glossary entries that follow are informal descriptions of some major features of the organisms described in Part Seven of this book. Each entry gives the group’s common name, followed by the formal scientific name of the group (in parentheses). Numbers in square brackets reference the location of the respective groups on the tree.

It is sometimes convenient to use an informal name to refer to a collection of organisms that are not monophyletic but nonetheless all share (or all lack) some common attribute. We call these “convenience terms”; such groups are indicated in these entries by quotation marks, and we do not give them formal scientific names. Examples include “prokaryotes,” “protists,” and “algae.” Note that these groups cannot be removed with a single cut; they represent a collection of distantly related groups that appear in different parts of the tree. We also use quotation marks here to designate two groups of fungi that are not believed to be monophyletic.

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A

acorn worms (Enteropneusta) Benthic marine hemichordates [124] with an acorn-shaped proboscis, a short collar (neck), and a long trunk.

actinobacteria (Actinobacteria) [7] Gram-positive bacteria [2] with genomes that have a high ratio of G-C to A-T nucleotide base pairs.

“algae” Convenience term encompassing various distantly related groups of aquatic, photosynthetic eukaryotes [17].

alveolates (Alveolata) [18] Unicellular eukaryotes with a layer of flattened vesicles (alveoli) supporting the plasma membrane. Major groups include the dinoflagellates [54], apicomplexans [53], and ciliates [52].

amborella (Amborella) [81] An understory shrub or small tree found only on the South Pacific island of New Caledonia. Thought to be the sister group of the remaining living angiosperms [28].

ambulacrarians (Ambulacraria) [41] The echinoderms [123] and hemichordates [124].

amniotes (Amniota) [49] Mammals, reptiles, and their extinct close relatives. Characterized by many adaptations to terrestrial life, including an amniotic egg (with a unique set of membranes—the amnion, chorion, and allantois), a water-repellant epidermis (with epidermal scales, hair, or feathers), and, in males, a penis that allows internal fertilization.

amoebozoans (Amoebozoa) [87] A group of eukaryotes [17] that use lobe-shaped pseudopods for locomotion and to engulf food. Major amoebozoan groups include the loboseans, plasmodial slime molds, and cellular slime molds.

amphibians (Amphibia) [133] Tetrapods [48] with glandular skin that lacks epidermal scales, feathers, or hair. Many amphibian species undergo a complete metamorphosis from an aquatic larval form to a terrestrial adult form, although direct development is also common. Major amphibian groups include frogs and toads (anurans), salamanders, and caecilians.

amphipods (Amphipoda) Small crustaceans [121] that are abundant in many marine and freshwater habitats. They are important herbivores, scavengers, and micropredators, and are an important food source for many aquatic organisms.

angiosperms (Anthophyta or Magnoliophyta) [28] The flowering plants. Major angiosperm groups include the monocots [85], eudicots [86], and magnoliids [84].

animals (Animalia or Metazoa) [32] Multicellular heterotrophic eukaryotes. The majority of animals are bilaterians [35]. Other groups of animals include the sponges [33], ctenophores [95], placozoans [99], and cnidarians [100]. The closest living relatives of the animals are the choanoflagellates [94].

annelids (Annelida) [110] Segmented worms, including earthworms, leeches, and polychaetes. One of the major groups of lophotrochozoans [37].

anthozoans (Anthozoa) One of the major groups of cnidarians [100]. Includes the sea anemones, sea pens, and corals.

anurans (Anura) Comprising the frogs and toads, this is the largest group of living amphibians [133]. They are tail-less, with a shortened vertebral column and elongate hind legs modified for jumping. Many species have an aquatic larval form known as a tadpole.

apicomplexans (Apicomplexa) [53] Parasitic alveolates [18] characterized by the possession of an apical complex at some stage in the life cycle.

arachnids (Arachnida) Chelicerates [119] with a body divided into two parts: a cephalothorax that bears six pairs of appendages (four pairs of which are usually used as legs) and an abdomen that bears the genital opening. Familiar arachnids include spiders, scorpions, mites and ticks, and harvestmen.

arbuscular mycorrhizal fungi (Glomeromycota) [91] A group of fungi [30] that associate with plant roots in a close symbiotic relationship.

archaeans (Archaea) [3] One of the two primary divisions of life [1]. The term is often used only for the prokaryotic archaeans, which are unicellular organisms that lack a nucleus and lack peptidoglycan in the cell wall. Recent studies indicate that eukaryotes [17] are most closely related to the lokiarchaeotes [12] among the prokaryotic archaeans.

archosaurs (Archosauria) [51] A group of reptiles [50] that includes dinosaurs and crocodilians [138]. Most dinosaur groups became extinct at the end of the Cretaceous; birds [137] are the only surviving dinosaurs.

arrow worms (Chaetognatha) [101] Small planktonic or benthic predatory marine worms with fins and a pair of hooked, prey-grasping spines on each side of the head.

arthropods (Arthropoda) The largest group of ecdysozoans [38]. Arthropods are characterized by a stiff exoskeleton, segmented bodies, and jointed appendages. Includes the chelicerates [119], myriapods [120], crustaceans [121], and hexapods (insects and their relatives) [122].

ascidians (Ascidiacea) “Sea squirts”; the largest group of tunicates [126]. They are sessile (as adults), marine, saclike filter feeders.

B

bacteria (Bacteria or Eubacteria) [2] Unicellular organisms lacking a nucleus, possessing distinctive ribosomes and initiator tRNA, and generally containing peptidoglycan in the cell wall. Different bacterial groups are distinguished primarily on nucleotide sequence data. One of the two primary divisions of life [1].

barnacles (Cirripedia) Crustaceans [121] that undergo two metamorphoses—first from a feeding planktonic larva to a nonfeeding swimming larva, and then to a sessile adult that forms a “shell” composed of four to eight plates cemented to a hard substrate.

bilaterians (Bilateria) [35] Those animal groups characterized by bilateral symmetry and three distinct tissue types (endoderm, ectoderm, and mesoderm). Includes the protostomes [36] and deuterostomes [41].

birds (Aves) [137] Feathered, flying (or secondarily flightless) tetrapods [48].

bivalves (Bivalvia) Major mollusk [111] group; clams and mussels. Bivalves typically have two similar hinged shells that are each asymmetrical across the midline.

bony vertebrates (Osteichthyes) [46] Vertebrates [44] in which the skeleton is usually ossified to form bone. Includes the ray-finned fishes [130], coelacanths [131], lungfishes [132], and tetrapods [48].

brachiopods (Brachiopoda) [108] Lophotrochozoans [37] with two similar hinged shells that are each symmetrical across the midline. Superficially resemble bivalve mollusks, except for the shell symmetry.

brittle stars (Ophiuroidea) Echinoderms [123] with five long, whip-like arms radiating from a distinct central disk that contains the reproductive and digestive organs.

brown algae (Phaeophyta) [57] Multicellular, almost exclusively marine stramenopiles [19] generally containing the pigment fucoxanthin as well as chlorophylls a and c in their chloroplasts.

bryozoans (Ectoprocta or Bryozoa) [102] A group of marine and freshwater lophotrochozoans [37] that live in colonies attached to substrates; also known as ectoprocts or moss animals. They are the sister group of entoprocts.

C

caecilians (Gymnophiona) A group of burrowing or aquatic amphibians [133]. They are elongate, legless, with a short tail (or none at all), reduced eyes covered with skin or bone, and a pair of sensory tentacles on the head.

calcareous sponges (Calcarea) [98] Filter-feeding marine sponges with spicules composed of calcium carbonate.

cellular slime molds (Dictyostelida) Amoebozoans [87] in which individual amoebas aggregate under stress to form a multicellular pseudoplasmodium.

cephalochordates (Cephalochordata) [125] See lancelets.

cephalopods (Cephalopoda) Active, predatory mollusks [111] in which the molluscan foot has been modified into muscular hydrostatic arms or tentacles. Includes octopuses, squids, and nautiluses.

cercozoans (Cercozoa) [59] Unicellular eukaryotes [17] that feed by means of threadlike pseudopods. Group together with foraminiferans [60] and radiolarians [58] to comprise the rhizarians [20].

charophytes (Charales) [70] See stoneworts.

chelicerates (Chelicerata) [119] A major group of arthropods [39] with pointed appendages (chelicerae) used to grasp food (as opposed to the chewing mandibles of most other arthropods). Includes the arachnids, horseshoe crabs, pycnogonids, and extinct sea scorpions.

chimaeras (Holocephali) A group of bottom-dwelling, marine, scaleless chondrichthyan fishes [129] with large, permanent, grinding tooth plates (rather than the replaceable teeth found in other chondrichthyans).

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chitons (Polyplacophora) Flattened, slow-moving mollusks [111] with a dorsal protective calcareous covering made up of eight articulating plates.

chlamydias (Chlamydiae) [10] A group of very small Gram-negative bacteria; they live as intracellular parasites of other organisms.

chlorophytes (Chlorophyta) [68] The most abundant and diverse group of green algae, including freshwater, marine, and terrestrial forms; some are unicellular, others colonial, and still others multicellular. Chlorophytes use chlorophylls a and c in their photosynthesis.

choanoflagellates (Choanozoa) [94] Unicellular eukaryotes [17] with a single flagellum surrounded by a collar. Most are sessile, some are colonial. The closest living relatives of the animals [32].

chondrichthyans (Chondrichthyes) [129] One of the two main groups of jawed vertebrates [45]; includes sharks, rays, and chimaeras. They have cartilaginous skeletons and paired fins.

chordates (Chordata) [43] One of the two major groups of deuterostomes [41], characterized by the presence (at some point in development) of a notochord, a hollow dorsal nerve cord, and a post-anal tail. Includes the lancelets [125], tunicates [126], and vertebrates [44].

“chytrids” [89] Convenience term used for a paraphyletic group of mostly aquatic, microscopic fungi [30] with flagellated gametes. Some exhibit alternation of generations.

ciliates (Ciliophora) [52] Alveolates [18] with numerous cilia and two types of nuclei (micronuclei and macronuclei).

clitellates (Clitellata) Annelids [110] with gonads contained in a swelling (called a clitellum) toward the head of the animal. Includes earthworms (oligochaetes) and leeches.

club fungi (Basidiomycota) [93] Fungi [30] that, if multicellular, bear the products of meiosis on club-shaped basidia and possess a long-lasting dikaryotic stage. Some are unicellular.

club mosses (Lycopodiophyta) [74] Vascular plants [25] characterized by microphylls. See lycophytes.

cnidarians (Cnidaria) [100] Aquatic, mostly marine eumetazoans [34] with specialized stinging organelles (nematocysts) used for prey capture and defense, and a blind gastrovascular cavity. The sister group of the bilaterians [35].

coelacanths (Actinista) [131] A group of marine lobe-limbed vertebrates [47] that was diverse from the Middle Devonian to the Cretaceous, but is now known from just two living species. The pectoral and anal fins are on fleshy stalks supported by skeletal elements, so they are also called lobe-finned fishes.

coleochaetophytes (Coleochaetales) [69] Multicellular green algae characterized by flattened growth form composed of thin-walled cells. Thought to be the sister-group to the stoneworts [70] plus land plants [24].

conifers (Pinophyta or Coniferophyta) [80] Cone-bearing, woody seed plants [26].

copepods (Copepoda) Small, abundant crustaceans [121] found in marine, freshwater, or wet terrestrial habitats. They have a single eye, long antennae, and a body shaped like a teardrop.

craniates (Craniata) Some biologist exclude the hagfishes [127] from the vertebrates [44], and use the term craniates to refer to the two groups combined.

crenarchaeotes (Crenarchaeota) [15] A major and diverse group of prokaryotic archaeans [3], defined on the basis of rRNA base sequences. Many are extremophiles (inhabit extreme environments), but the group may also be the most abundant archaeans in the marine environment.

crinoids (Crinoidea) Echinoderms [123] with a mouth surrounded by feeding arms, and a U-shaped gut with the mouth next to the anus. They attach to the substratum by a stalk or are free-swimming. Crinoids were abundant in the middle and late Paleozoic, but only a few hundred species have survived to the present. Includes the sea lilies and feather stars.

crocodilians (Crocodylia) [138] A group of large, predatory, aquatic archosaurs [51]. The closest living relatives of birds [137]. Includes alligators, caimans, crocodiles, and gharials.

crustaceans (Crustacea) [121] Major group of marine, freshwater, and terrestrial arthropods [39] with a head, thorax, and abdomen (although the head and thorax may be fused), covered with a thick exoskeleton, and with two-part appendages. Crustaceans undergo metamorphosis from a nauplius larva. Includes decapods, isopods, krill, barnacles, amphipods, copepods, and ostracods.

ctenophores (Ctenophora) [95] Radially symmetrical, gelatinous marine animals [32], with eight rows of fused plates of cilia (called ctenes).

cyanobacteria (Cyanobacteria) [8] A group of unicellular, colonial, or filamentous bacteria that conduct photosynthesis using chlorophyll a.

cycads (Cycadophyta) [77] Palmlike gymnosperms with large, compound leaves.

cyclostomes (Cyclostomata) This term refers to the possibly monophyletic group of lampreys [128] and hagfishes [127]. Molecular data support this group, but morphological data suggest that lampreys are more closely related to jawed vertebrates [45] than to hagfishes.

D

decapods (Decapoda) A group of marine, freshwater, and semiterrestrial crustaceans [121] in which five of the eight pairs of thoracic appendages function as legs (the other three pairs, called maxillipeds, function as mouthparts). Includes crabs, lobsters, crayfishes, and shrimps.

demosponges (Demospongiae) [97] The largest of the three groups of sponges [33], accounting for 90 percent of all sponge species. Demosponges have spicules made of silica, spongin fiber (a protein), or both.

deuterostomes (Deuterostomia) [41] One of the two major groups of bilaterians [35], in which the mouth forms at the opposite end of the embryo from the blastopore in early development (contrast with protostomes). Includes the ambulacrarians [42] and chordates [43].

diatoms (Bacillariophyta) [56] Unicellular, photosynthetic stramenopiles [19] with glassy cell walls in two parts.

dikaryotic fungi (Dikarya) [31] A group of fungi [30] in which two genetically different haploid nuclei coexist and divide within the same hypha; includes club fungi [93] and sac fungi [92].

dinoflagellates (Dinoflagellata) [54] A group of alveolates [18] usually possessing two flagella, one in an equatorial groove and the other in a longitudinal groove; many are photosynthetic.

dinosaurs (Dinosauria) A group of archosaurs [51] that includes birds [137] as well as many extinct groups from the Mesozoic era. Extinct Mesozoic dinosaurs included some of the largest terrestrial vertebrates that have ever lived. Informally, many people use the term to refer only to the extinct Mesozoic species.

diplomonads (Diplomonadida) [61] A group of eukaryotes [17] lacking mitochondria; most have two nuclei, each with four associated flagella.

dry-nosed primates (Haplorhini) A group of primate mammals [134] that includes apes, monkeys, and tarsiers.

E

ecdysozoans (Ecdysozoa) [38] One of the two major groups of protostomes [36], characterized by periodic molting of their exoskeletons. Nematodes [116] and arthropods [39] are the largest ecdysozoan groups.

echinoderms (Echinodermata) [123] A major group of marine deuterostomes [41] with fivefold radial symmetry (at some stage of life) and an endoskeleton made of calcified plates and spines. Includes sea stars, crinoids, sea urchins, sea cucumbers, and brittle stars.

elasmobranchs (Elasmobranchii) The largest group of chondrichthyan fishes [129]. Includes sharks, skates, and rays. In contrast to the other group of living chondrichthyans (the chimaeras), they have replaceable teeth.

embryophytes See land plants [24].

entoprocts (Entoprocta) [103] A group of marine and freshwater lophotrochozoans [37] that live as single individuals or in colonies attached to substrates. They are the sister group of bryozoans, from which they differ in having both their mouth and anus inside the lophophore (the anus is outside the lophophore in bryozoans).

eudicots (Eudicotyledones) [86] A group of angiosperms [28] with pollen grains possessing three openings. Typically with two cotyledons, net-veined leaves, taproots, and floral organs typically in multiples of four or five.

euglenids (Euglenida) [64] Flagellate excavates characterized by a pellicle composed of spiraling strips of protein under the plasma membrane; the mitochondria have disk-shaped cristae. Some are photosynthetic.

eukaryotes (Eukarya) [17] Organisms made up of one or more complex cells in which the genetic material is contained in nuclei. Contrast with archaeans [3] and bacteria [2].

eumetazoans (Eumetazoa) [34] A group of animals [32] characterized by body symmetry, a gut, a nervous system, specialized types of cell junctions, and well-organized tissues in distinct cell layers.

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euphyllophytes (Euphyllophyta) The group of vascular plants [25] that is sister to the lycophytes [74] and which includes all plants with megaphylls.

euryarchaeotes (Euryachaeota) [16] A major group of prokaryotic archaeans [3], diagnosed on the basis of rRNA sequences. Includes many methanogens, extreme halophiles, and thermophiles.

eutherians (Eutheria) A group of viviparous mammals [134], eutherians are well developed at birth (contrast to prototherians and marsupials, the other two groups of mammals). Most familiar mammals outside the Australian and South American regions are eutherians (see Table 32.1).

excavates (Excavata) [21] Diverse group of unicellular, flagellate eukaryotes, many of which possess a feeding groove; some lack mitochondria.

F

ferns (Pteridopsida or Polypodiopsida) [76] Vascular plants [25] usually possessing large, frond-like leaves and possessing thin-walled sporangia.

firmicutes (Firmicutes) [6] Mostly Gram-positive bacteria [2] with genomes that have a low ratio of G-C to A-T nucleotide base pairs.

flatworms (Platyhelminthes) [104] A group of dorsoventrally flattened and generally elongate soft-bodied lophotrochozoans [37]. May be free-living or parasitic, found in marine, freshwater, or damp terrestrial environments. Major flatworm groups include the tapeworms, flukes, monogeneans, and turbellarians.

flowering plants See angiosperms [28].

flukes (Trematoda) A group of wormlike parasitic flatworms [104] with complex life cycles that involve several different host species. May be paraphyletic with respect to tapeworms.

foraminiferans (Foraminifera) [60] Amoeboid organisms with fine, branched pseudopods that form a food-trapping net. Most produce external shells of calcium carbonate.

fungi (Fungi) [30] Eukaryotic heterotrophs with absorptive nutrition based on extracellular digestion; cell walls contain chitin. Major fungal groups include the microsporidia [88], “chytrids” [89], “zygospore fungi” [90], arbuscular mycorrhizal fungi [91], sac fungi [92], and club fungi [93].

G

gastropods (Gastropoda) The largest group of mollusks [111]. Gastropods possess a well-defined head with two or four sensory tentacles (often terminating in eyes) and a ventral foot. Most species have a single coiled or spiraled shell. Common in marine, freshwater, and terrestrial environments.

gastrotrichs (Gastrotricha) [106] Tiny (0.06–3.0 mm), elongate acoelomate lophotrochozoans [37] that are covered in cilia. They live in marine, freshwater, and wet terrestrial habitats. They are simultaneous hermaphrodites.

ginkgo (Ginkgophyta) [78] A gymnosperm [27] group with only one living species. The ginkgo seed is surrounded by a fleshy tissue not derived from an ovary wall and hence not a fruit.

glass sponges (Hexactinellida) [96] Sponges [33] with a skeleton composed of four- and/or six-pointed spicules made of silica.

glaucophytes (Glaucophyta) [66] Unicellular freshwater algae with chloroplasts containing traces of peptidoglycan, the characteristic cell wall material of bacteria.

gnathostomes (Gnathostomata) See jawed vertebrates [45].

gnetophytes (Gnetophyta) [79] A gymnosperm [27] group with three very different lineages; all have wood with vessels, unlike other gymnosperms.

Gram-negative bacteria Bacteria [2] with a very thin peptidoglycan layer surrounded by an outer membrane, which together make up the cell envelope.

Gram-positive bacteria Bacteria [2] with a thick, uniform cell wall made up of a meshwork of peptidoglycan.

green plants (Viridiplantae) [23] Organisms with chlorophylls a and b, cellulose-containing cell walls, starch as a carbohydrate storage product, and chloroplasts surrounded by two membranes.

gymnosperms (Gymnospermae) [27] Seed plants [26] with seeds “naked” (i.e., not enclosed in carpels). Probably monophyletic, but status still in doubt. Includes the conifers [80], gnetophytes [79], ginkgo [78], and cycads [77].

H

hadobacteria (Hadobacteria) [4] A group of extremophilic bacteria [2] that includes the genera Deinococcus and Thermus.

hagfishes (Myxini) [127] Elongate, slimy-skinned vertebrates [44] with three small accessory hearts, a partial cranium, and no stomach or paired fins. See also craniata; cyclostomes.

hemichordates (Hemichordata) [124] One of the two primary groups of ambulacrarians [42]; marine wormlike organisms with a three-part body plan.

heteroloboseans (Heterolobosea) [63] Colorless excavates [21] that can transform among amoeboid, flagellate, and encysted stages.

hexapods (Hexapoda) [122] Major group of arthropods [39] characterized by a reduction (from the ancestral arthropod condition) to six walking appendages, and the consolidation of three body segments to form a thorax. Includes insects and their relatives (see Table 31.2).

holometabolous insects The group of hexapods [122] that undergoes complete metamorphosis.

hornworts (Anthocerophyta) [73] Nonvascular plants with sporophytes that grow from the base. Cells contain a single large, platelike chloroplast.

horsehair worms (Nematomorpha) [115] A group of very thin, elongate, wormlike freshwater ecdysozoans [38]. Largely nonfeeding as adults, they are parasites of insects and crayfish as larvae.

horseshoe crabs (Xiphosura) Marine chelicerates [119] with a large outer shell in three parts: a carapace, an abdomen, and a tail-like telson. There are only five living species, but many additional species are known from fossils.

horsetails (Sphenophyta or Equisetophyta) [75] Vascular plants [25] with reduced megaphylls in whorls.

hydrozoans (Hydrozoa) A group of cnidarians [100]. Most species go through both polyp and medusa stages, although one stage or the other is eliminated in some species.

hyperthermophilic bacteria [5] A group of thermophilic bacteria [2] that live in volcanic vents, hot springs, and in underground oil reservoirs; includes the genera Aquifex and Thermotoga.

I

insects (Insecta) The largest group within the hexapods [122]. Insects are characterized by exposed mouthparts and one pair of antennae containing a sensory receptor called a Johnston’s organ. Most have two pairs of wings as adults. There are more described species of insects than all other groups of life [1] combined, and many species remain to be discovered. The major insect groups are described in Table 31.2.

“invertebrates” Convenience term encompassing any animal [32] that is not a vertebrate [44].

isopods (Isopoda) Crustaceans [121] characterized by a compact head, unstalked compound eyes, and mouthparts consisting of four pairs of appendages. Isopods are abundant and widespread in salt, fresh, and brackish water, although some species (the sow bugs) are terrestrial.

J

jawed vertebrates (Gnathostomata) [45] A major group of vertebrates [44] with jawed mouths. Includes chondrichthyans [129], ray-finned fishes [130], and lobe-limbed vertebrates [47].

K

kinetoplastids (Kinetoplastida) [65] Unicellular, flagellate organisms characterized by the presence in their single mitochondrion of a kinetoplast (a structure containing multiple, circular DNA molecules).

kinorhynchs (Kinorhyncha) [113] Small (< 1 mm) marine ecdysozoans [38] with bodies in 13 segments and a retractable proboscis.

korarchaeotes (Korarchaeota) A group of prokaryotic archaeans [3] known only by evidence from nucleic acids derived from hot springs.

krill (Euphausiacea) A group of shrimplike marine crustaceans [121] that are important components of the zooplankton.

L

lampreys (Petromyzontiformes) [128] Elongate, eel-like vertebrates [44] that often have rasping and sucking disks for mouths.

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lancelets (Cephalochordata) [125] A group of weakly swimming, eel-like benthic marine chordates [43].

land plants (Embryophyta) [24] Plants with embryos that develop within protective structures; also called embryophytes. Both sporophytes and gametophytes of land plants are multicellular. Land plants possess a cuticle. Major groups are the liverworts [71], mosses [72], hornworts [73], and vascular plants [25].

larvaceans (Larvacea) Solitary, planktonic tunicates [126] that retain both notochords and nerve cords throughout their lives.

lepidosaurs (Lepidosauria) [135] Reptiles [50] with overlapping scales. Includes tuataras and squamates (lizards, snakes, and amphisbaenians).

life (Life) [1] The monophyletic group that includes all known living organisms. Characterized by a nucleic-acid based genetic system (DNA or RNA), metabolism, and cellular structure. Some parasitic forms, such as viruses, have secondarily lost some of these features and rely on the cellular environment of their host.

liverworts (Hepatophyta) [71] Nonvascular plants lacking stomata; stalk of sporophyte elongates along its entire length.

lobe-limbed vertebrates (Sarcopterygii) [47] One of the two major groups of bony vertebrates [46], characterized by jointed appendages (paired fins or limbs).

loboseans (Lobosea) A group of unicellular amoebozoans [87]; includes the most familiar amoebas (e.g., Amoeba proteus).

lokiarchaeotes (Lokiarchaeota) [12] A group of prokaryotic archaeans [3] known from deep-sea hydrothermal vents, Among the known prokaryotic archaeans, they are the closest relatives of the eukaryotes [17].

“lophophorates” Convenience term used to describe several groups of lophotrochozoans [37] that have a feeding structure called a lophophore (a circular or U-shaped ridge around the mouth that bears one or two rows of ciliated, hollow tentacles). Not a monophyletic group.

lophotrochozoans (Lophotrochozoa) [37] One of the two main groups of protostomes [36]. This group is morphologically diverse, and is supported primarily on information from gene sequences. Includes bryozoans and entoprocts [103], flatworms [104], rotifers and gastrotrichs [106], ribbon worms [107], brachiopods [108], phoronids [109], annelids [110], and mollusks [111].

loriciferans (Loricifera) [114] Small (< 1 mm) ecdysozoans [38] with bodies in four parts, covered with six plates.

lungfishes (Dipnoi) [132] A group of aquatic lobe-limbed vertebrates [47] that are the closest living relatives of the tetrapods [48]. They have a modified swim bladder used to absorb oxygen from air, so some species can survive the temporary drying of their habitat.

lycophytes (Lycopodiophyta) [74] Vascular plants [25] characterized by microphylls; includes club mosses, spike mosses, and quillworts.

M

magnoliids (Magnoliidae) [84] A major group of angiosperms [28] possessing two cotyledons and pollen grains with a single opening. The group is defined primarily by nucleotide sequence data; it is more closely related to the eudicots and monocots than to three other small angiosperm groups.

mammals (Mammalia) [134] A group of tetrapods [48] with hair covering all or part of their skin; females produce milk to feed their developing young. Includes the prototherians, marsupials, and eutherians.

mandibulates (Mandibulata) [40] Arthropods [39] that include mandibles as mouth parts. Includes myriapods [120], crustaceans [121], and hexapods [122].

marsupials (Marsupialia) Mammals [134] in which the female typically has a marsupium (a pouch for rearing young, which are born at an extremely early stage in development). Includes such familiar mammals as opossums, koalas, and kangaroos.

metazoans (Metazoa) See animals [32].

microbial eukaryotes See “protists.”

microsporidia (Microsporidia) [88] A group of parasitic unicellular fungi [30] that lack mitochondria and have walls that contain chitin.

mollusks (Mollusca) [111] One of the major groups of lophotrochozoans [37], mollusks have bodies composed of a foot, a mantle (which often secretes a hard, calcareous shell), and a visceral mass. Includes monoplacophorans, chitons, bivalves, gastropods, and cephalopods.

monilophytes (Monilophyta) A group of vascular plants [25], sister to the seed plants [26], characterized by overtopping and possession of megaphylls; includes the horsetails [75] and ferns [76].

monocots (Monocotyledones) [85] Angiosperms [28] characterized by possession of a single cotyledon, usually parallel leaf veins, a fibrous root system, pollen grains with a single opening, and floral organs usually in multiples of three.

monogeneans (Monogenea) A group of ectoparasitic flatworms [104].

monoplacophorans (Monoplacophora) Mollusks [111] with segmented body parts and a single, thin, flat, rounded, bilateral shell.

mosses (Bryophyta) [72] Nonvascular plants with true stomata and erect, “leafy” gametophytes; sporophytes elongate by apical cell division.

moss animals See bryozoans [102].

mycoplasmas Firmicutes [6] that lack cell walls and are among the smallest known cellular organisms.

myriapods (Myriapoda) [120] Arthropods [39] characterized by an elongate, segmented trunk with many legs. Includes centipedes and millipedes.

N

nanoarchaeotes (Nanoarchaeota) A group of extremely small, thermophilic, prokaryotic archaeans [3] with a much-reduced genome. The only described example can survive only when attached to a host organism.

nematodes (Nematoda) [116] A very large group of elongate, unsegmented ecdysozoans [38] with thick, multilayer cuticles. They are among the most abundant and diverse animals, although most species have not yet been described. Include free-living predators and scavengers, as well as parasites of most species of land plants [24] and animals [32].

neognaths (Neognathae) The main group of birds [137], including all living species except the ostrich, emu, rheas, kiwis, cassowaries, and tinamous. See palaeognaths.

neopterans (Neoptera) The largest group of flying (winged) hexapods [122], recognizable by the fact that they can fold their wings out of the way upon landing.

O

oligochaetes (Oligochaeta) Annelid [110] group whose members lack parapodia, eyes, and anterior tentacles, and have few setae. Earthworms are the most familiar oligochaetes.

onychophorans (Onychophora) [118] Elongate, segmented ecdysozoans [38] with many pairs of soft, unjointed, claw-bearing legs. Also known as velvet worms.

oomycetes (Oomycota) [55] Water molds and relatives; absorptive heterotrophs with nutrient-absorbing, filamentous hyphae.

opisthokonts (Opisthokonta) [29] A group of eukaryotes [17] in which the flagellum on motile cells, if present, is posterior. The opisthokonts include the fungi [30], animals [32], and choanoflagellates [94].

ostracods (Ostracoda) Marine and freshwater crustaceans [121] that are laterally compressed and protected by two clamlike calcareous or chitinous shells.

P

palaeognaths (Palaeognathae) A group of secondarily flightless or weakly flying birds [137]. Includes the flightless ostrich, emu, rheas, kiwis, and cassowaries, and the weakly flying tinamous.

parabasalids (Parabasalia) [62] A group of unicellular eukaryotes [17] that lack mitochondria; they possess flagella in clusters near the anterior of the cell.

phoronids (Phoronida) [109] A small group of sessile, wormlike marine lophotrochozoans [37] that secrete chitinous tubes and feed using a lophophore.

placoderms (Placodermi) An extinct group of jawed vertebrates [45] that lacked teeth. Placoderms were the dominant predators in Devonian oceans.

placozoans (Placozoa) [99] A poorly known group of structurally simple, asymmetrical, flattened, transparent animals found in coastal marine tropical and subtropical seas. Most evidence suggests that placozoans are secondarily simplified eumetazoans [34].

Plantae (Plantae) [22] The most broadly defined plant group, corresponding to the group that descended from the primary endosymbiotic event that gave rise to chloroplasts. Includes green plants [23] as well as glaucophytes [66] and red algae [67]. In most parts of this book, we use the word plant as synonymous with land plant [24], a more restrictive definition.

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plasmodial slime molds (Myxogastrida) Amoebozoans [87] that in their feeding stage consist of a coenocyte called a plasmodium.

pogonophorans (Pogonophora) Deep-sea annelids [110] that lack a mouth or digestive tract; they feed by taking up dissolved organic matter, facilitated by endosymbiotic bacteria in a specialized organ (the trophosome).

polychaetes (Polychaeta) A group of mostly marine annelids [110] with one or more pairs of eyes and one or more pairs of feeding tentacles; parapodia and setae extend from most body segments. May be paraphyletic with respect to the clitellates.

priapulids (Priapulida) [112] A small group of cylindrical, unsegmented, wormlike marine ecdysozoans [38] that takes its name from its phallic appearance.

primates (Primates) A group of mammals [134] that includes apes, monkeys, tarsiers, lemurs, and lorises.

“prokaryotes” Not a monophyletic group; as commonly used, includes the bacteria [2] and prokaryotic archaeans [3]. A term of convenience encompassing all cellular organisms that are not eukaryotes.

progymnosperms (Progymnospermophyta) An extinct group of seedless, vascular plants [25] that were among the first large, woody trees; lived in the Middle Devonian and Early Carboniferous periods.

proteobacteria (Proteobacteria) [11] A large and extremely diverse group of Gram-negative bacteria that includes many pathogens, nitrogen fixers, and photosynthesizers. Includes the alpha, beta, gamma, delta, and epsilon proteobacteria.

“protists” This term of convenience is used to encompass a large number of distinct and distantly related groups of eukaryotes, many but far from all of which are microbial and unicellular. Essentially a “catch-all” term for any eukaryote group not contained within the land plants [24], fungi [30], or animals [32].

protostomes (Protostomia) [36] One of the two major groups of bilaterians [35]. In protostomes, the mouth typically forms from the blastopore (if present) in early development (contrast with deuterostomes). The major protostome groups are the lophotrochozoans [37] and ecdysozoans [38].

prototherians (Prototheria) A mostly extinct group of mammals [134], common during the Cretaceous and early Cenozoic. The five living species—four echidnas and the duck-billed platypus—are the only extant egg-laying mammals.

pterobranchs (Pterobranchia) A small group of sedentary marine hemichordates [124] that live in tubes secreted by the proboscis. They have one to nine pairs of arms, each bearing long tentacles that capture prey and function in gas exchange.

pterygotes (Pterygota) Flying (winged) insects, the largest group of hexapods [122].

pycnogonids (Pycnogonida) Treated in this book as a group of chelicerates [119], but sometimes considered an independent group of arthropods [39]. Pycnogonids have reduced bodies and very long, slender legs. Also called sea spiders.

R

radiolarians (Radiolaria) [58] Amoeboid organisms with needlelike pseudopods supported by microtubules. Most have glassy internal skeletons.

ray-finned fishes (Actinopterygii) [130] A highly diverse group of freshwater and marine bony vertebrates [46]. They have reduced swim bladders that often function as hydrostatic organs and fins supported by soft rays (lepidotrichia). Includes most familiar fishes.

red algae (Rhodophyta) [67] Mostly multicellular, marine and freshwater algae characterized by the presence of phycoerythrin in their chloroplasts.

reptiles (Reptilia) [50] One of the two major groups of extant amniotes [49], supported on the basis of similar skull structure and gene sequences. The term “reptiles” traditionally excluded the birds [137], but the resulting group is then clearly paraphyletic. As used in this book, the reptiles include turtles [136], lepidosaurs [135], birds [137], and crocodilians [138].

rhizarians (Rhizaria) [20] Mostly amoeboid unicellular eukaryotes with pseudopods, many with external or internal shells. Includes the foraminiferans [60], cercozoans [59], and radiolarians [58].

rhyniophytes (Rhyniophyta) A group of early vascular plants [25] that appeared in the Silurian and became extinct in the Devonian. Possessed dichotomously branching stems with terminal sporangia but no true leaves or roots.

ribbon worms (Nemertea) [107] A group of unsegmented lophotrochozoans [37] with an eversible proboscis used to capture prey. Mostly marine, but some species live in fresh water or on land.

rotifers (Rotifera) [105] Tiny (< 0.5 mm) lophotrochozoans [37] with a pseudocoelomic body cavity that functions as a hydrostatic organ, and a ciliated feeding organ called the corona that surrounds the head. Rotifers live in freshwater and wet terrestrial habitats.

roundworms (Nematoda) [116] See nematodes.

S

sac fungi (Ascomycota) [92] Fungi that bear the products of meiosis within sacs (asci) if the organism is multicellular. Some are unicellular.

salamanders (Caudata) A group of amphibians [133] with distinct tails in both larvae and adults and limbs set at right angles to the body.

salps See thaliaceans.

sarcopterygians (Sarcopterygii) [47] See lobe-limbed vertebrates.

scyphozoans (Scyphozoa) Marine cnidarians [100] in which the medusa stage dominates the life cycle. Commonly known as jellyfish.

sea cucumbers (Holothuroidea) Echinoderms [123] with an elongate, cucumber-shaped body and leathery skin. They are scavengers on the ocean floor.

sea spiders See pycnogonids.

sea squirts See ascidians.

sea stars (Asteroidea) Echinoderms [123] with five (or more) fleshy “arms” radiating from an indistinct central disk. Also called starfishes.

sea urchins (Echinoidea) Echinoderms [123] with a test (shell) that is covered in spines. Most are globular in shape, although some groups (such as the sand dollars) are flattened.

“seed ferns” A paraphyletic group of loosely related, extinct seed plants that flourished in the Devonian and Carboniferous. Characterized by large, frondlike leaves that bore seeds.

seed plants (Spermatophyta) [26] Heterosporous vascular plants [25] that produce seeds; most produce wood; branching is axillary (not dichotomous). The major seed plant groups are gymnosperms [27] and angiosperms [28].

simians (Simiiformes) A group of primate mammals [134] that consists of apes and monkeys.

sow bugs See isopods.

spirochetes (Spirochaetes) [9] Motile, Gram-negative bacteria with a helically coiled structure and characterized by axial filaments.

sponges (Porifera) [33] A group of relatively asymmetric, filter-feeding animals that lack a gut or nervous system and generally lack differentiated tissues. Includes glass sponges [96], demosponges [97], and calcareous sponges [98].

springtails (Collembola) Wingless hexapods [122] with springing structures on the third and fourth segments of their bodies. Springtails are extremely abundant in some environments (especially in soil, leaf litter, and vegetation).

squamates (Squamata) The major group of lepidosaurs [135], characterized by the possession of movable quadrate bones (which allow the upper jaw to move independently of the rest of the skull) and hemipenes (a paired set of eversible penises, or penes) in males. Includes the lizards (a paraphyletic group), snakes, and amphisbaenians.

staphylococci (Staphylococcus) Firmicutes [6] that are abundant on the surface of the human body; can cause skin diseases and respiratory, intestinal, and wound infections.

star anise (Austrobaileyales) [83] A group of woody angiosperms [28] thought to be the sister-group of the clade of flowering plants that includes eudicots [86], monocots [85], and magnoliids [84].

starfish (Asteroidea) See sea stars.

stoneworts (Charales) [70] Multicellular green algae with branching, apical growth and plasmodesmata between adjacent cells. The closest living relatives of the land plants [24], they retain the egg in the parent organism.

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stramenopiles (Heterokonta or Stramenopila) [19] Organisms having, at some stage in their life cycle, two unequal flagella, the longer possessing rows of tubular hairs. Chloroplasts, when present, surrounded by four membranes. Major stramenopile groups include the brown algae [57], diatoms [56], and oomycetes [55].

streptophytes (Streptophyta) All green plants [23] other than chlorophytes [68].

T

tapeworms (Cestoda) Parasitic flatworms [104] that live in the digestive tracts of vertebrates as adults, and usually in various other species of animals as juveniles.

tardigrades (Tardigrada) [117] Small (< 0.5 mm) ecdysozoans [38] with fleshy, unjointed legs and no circulatory or gas exchange organs. They live in marine sands, in temporary freshwater pools, and on the water films of plants. Also called water bears.

tetrapods (Tetrapoda) [48] The major group of lobe-limbed vertebrates [47]; includes the amphibians [133] and the amniotes [49]. Named for the presence of four jointed limbs (although limbs have been secondarily reduced or lost completely in several tetrapod groups).

thaliaceans (Thaliacea) A group of solitary or colonial planktonic marine tunicates [126]. Also called salps.

thaumarchaeotes (Thaumarchaeota) [14] A group of prokaryotic archaeans [3] known only from hot environments; they oxidize ammonia and are thought to play an important role in the nitrogen cycle.

therians (Theria) Mammals [134] characterized by viviparity (live birth). Includes eutherians and marsupials.

theropods (Theropoda) Archosaurs [51] with bipedal stance, hollow bones, a furcula (“wishbone”), elongated metatarsals with three-fingered feet, and a pelvis that points backwards. Includes many well-known extinct dinosaurs (such as Tyrannosaurus rex), as well as the living birds [137].

tracheophytes See vascular plants [25].

trilobites (Trilobita) An extinct group of arthropods [39] related to the chelicerates [119]. Trilobites flourished from the Cambrian through the Permian.

tuataras (Rhyncocephalia) A group of lepidosaurs [135] known mostly from fossils; there is only one living tuatara species. The quadrate bone of the upper jaw is fixed firmly to the skull. Sister group of the squamates.

tunicates (Tunicata) [126] A group of chordates [43] that are mostly saclike filter feeders as adults, with motile larval stages that resemble tadpoles.

turbellarians (Turbellaria) A group of free-living, generally carnivorous flatworms [104]. Their monophyly is questionable.

turtles (Testudines) [136] A group of reptiles [50] with a bony carapace (upper shell) and plastron (lower shell) that encase the body in a fashion unique among the vertebrates.

U

urochordates (Tunicata) [126] See tunicates.

V

vascular plants (Tracheophyta) [25] Plants with xylem and phloem. Major groups include the lycophytes [74] and euphyllophytes.

vertebrates (Vertebrata) [44] The largest group of chordates [43], characterized by a rigid endoskeleton supported by the vertebral column and an anterior skull encasing a brain. Includes hagfishes [127], lampreys [128], and the jawed vertebrates [45], although some biologists exclude the hagfishes from this group. See also craniates.

W

water bears See tardigrades.

water lilies (Nymphaeaceae) [82] A group of aquatic, freshwater angiosperms [28] that are rooted in soil in shallow water, with round floating leaves and flowers that extend above the water’s surface. They are the sister-group to most of the remaining flowering plants, with the exception of the genus Amborella [81].

wet-nosed primates (Strepsirrhini) A group of primate mammals [134] that includes lemurs and lorises.

X

xenoturbellids (Xenoturbellida) Wormlike organisms that feed on or parasitize marine mollusks. Relationships uncertain; thought to be a sister group of either ambulacrarians [42] or bilaterians [35].

Y

“yeasts” Convenience term for several distantly related groups of unicellular fungi [30].

Z

“zygospore fungi” (Zygomycota, if monophyletic) [90] A convenience term for a probably paraphyletic group of fungi [30] in which hyphae of differing mating types conjugate to form a zygosporangium.