Monophyletic in the context of Paleognaths

The green algae (sg.: green alga) are a group of chlorophyll-containing autotrophic algae consisting of the phylum Prasinodermophyta and its unnamed sister group that contains the Chlorophyta and Charophyta/Streptophyta. The land plants (Embryophyta) have emerged deep within the charophytes as a sister of the Zygnematophyceae. Since the realization that the Embryophyta emerged within the green algae, some authors are starting to include them. The completed clade that includes both green algae and embryophytes is monophyletic and is referred to as the clade Viridiplantae and as the kingdom Plantae. The green algae include unicellular and colonial flagellates, most with two flagella per cell, as well as various colonial, coccoid (spherical), and filamentous forms, and macroscopic, multicellular seaweeds. There are about 22,000 species of green algae, many of which live most of their lives as single cells, while other species form coenobia (colonies), long filaments, or highly differentiated macroscopic seaweeds.

A few other organisms rely on green algae to conduct photosynthesis for them. The chloroplasts in dinoflagellates of the genus Lepidodinium, euglenids and chlorarachniophytes were acquired from ingested endosymbiont green algae, and in the latter retain a nucleomorph (vestigial nucleus). Green algae are also found symbiotically in the ciliate Paramecium, and in Hydra viridissima and in flatworms. Some species of green algae, particularly of genera Trebouxia of the class Trebouxiophyceae and Trentepohlia (class Ulvophyceae), can be found in symbiotic associations with fungi to form lichens. In general, the fungal species that partner in lichens cannot live on their own, while the algal species is often found living in nature without the fungus. Trentepohlia is a filamentous green alga that can live independently on humid soil, rocks or tree bark or form the photosymbiont in lichens of the family Graphidaceae. Also the macroalga Prasiola calophylla (Trebouxiophyceae) is terrestrial, andPrasiola crispa, which live in the supralittoral zone, is terrestrial and can in the Antarctic form large carpets on humid soil, especially near bird colonies.

A fungus (pl.: fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as one of the traditional eukaryotic kingdoms, along with Animalia, Plantae, and either Protista or Protozoa and Chromista.

A characteristic that places fungi in a different kingdom from plants, bacteria, and some protists is chitin in their cell walls. Fungi, like animals, are heterotrophs; they acquire their food by absorbing dissolved organic molecules, typically by secreting digestive enzymes into their environment. Fungi do not photosynthesize. Growth is their means of mobility, except for spores (a few of which are flagellated), which may travel through the air or water. Fungi are the principal decomposers in ecological systems. These and other differences place fungi in a single group of related organisms, named the Eumycota (true fungi or Eumycetes), that share a common ancestor (i.e. they form a monophyletic group), an interpretation that is also strongly supported by molecular phylogenetics. This fungal group is distinct from the structurally similar myxomycetes (slime molds) and oomycetes (water molds). The discipline of biology devoted to the study of fungi is known as mycology (from the Greek μύκης, mykes 'mushroom'). In the past, mycology was regarded as a branch of botany, although it is now known that fungi are genetically more closely related to animals than to plants.

The gymnosperms (/ˈdʒɪmnəˌspɜːrmz, -noʊ-/ nə-spurmz, -⁠noh-; from Ancient Greek γυμνός (gumnós), meaning "naked", and σπέρμα (spérma), meaning "seed", and thus, "naked seed") are a group of woody, perennial seed-producing plants, typically lacking the protective outer covering which surrounds the seeds in flowering plants, that include conifers, cycads, Ginkgo, and gnetophytes, forming the clade Gymnospermae. The name is based on the unenclosed condition of their seeds (called ovules in their unfertilized state). The non-encased condition of their seeds contrasts with the seeds and ovules of flowering plants (angiosperms), which are enclosed within an ovary. Gymnosperm seeds develop either on the surface of scales or leaves, which are often modified to form cones, or on their own as in yew, Torreya, and Ginkgo.

The life cycle of a gymnosperm involves alternation of generations, with a dominant diploid sporophyte phase, and a reduced haploid gametophyte phase, which is dependent on the sporophytic phase. The term "gymnosperm" is often used in paleobotany to refer to (the paraphyletic group of) all non-angiosperm seed plants. In that case, to specify the modern monophyletic group of gymnosperms, the term Acrogymnospermae is sometimes used.

Equinae is a subfamily of the family Equidae, known from the Hemingfordian stage of the Early Miocene (16 million years ago) onwards. They originated in North America, before dispersing to every continent except Australia and Antarctica. They are thought to be a monophyletic grouping. Members of the subfamily are referred to as equines; the only extant equines are the horses, asses, and zebras of the genus Equus, with two other genera Haringtonhippus and Hippidion becoming extinct at the beginning of the Holocene, around 11–12,000 years ago.

The subfamily contains two tribes, the Equini and the Hipparionini, as well as two unplaced genera, Merychippus and Scaphohippus. Members of the family ancestrally had three toes, while members of the tribe Equini from the Middle Miocene onwards developed monodactyl feet.

Amphibians are ectothermic, anamniotic, four-limbed vertebrate animals that constitute the class Amphibia. In its broadest sense, it is a paraphyletic group encompassing all tetrapods, but excluding the amniotes (tetrapods with an amniotic membrane, such as modern reptiles, birds and mammals). All extant (living) amphibians belong to the monophyletic subclass Lissamphibia, with three living orders: Anura (frogs and toads), Urodela (salamanders), and Gymnophiona (caecilians). Evolved to be mostly semiaquatic, amphibians have adapted to inhabit a wide variety of habitats, with most species living in freshwater, wetland or terrestrial ecosystems (such as riparian woodland, fossorial and even arboreal habitats). Their life cycle typically starts out as aquatic larvae with gills known as tadpoles, but some species have developed behavioural adaptations to bypass this.

Young amphibians generally undergo metamorphosis from an aquatic larval form with gills to an air-breathing adult form with lungs. Amphibians use their skin as a secondary respiratory interface, and some small terrestrial salamanders and frogs even lack lungs and rely entirely on their skin. They are superficially similar to reptiles like lizards, but unlike reptiles and other amniotes, require access to water bodies to breed. With their complex reproductive needs and permeable skins, amphibians are often ecological indicators to habitat conditions; in recent decades there has been a dramatic decline in amphibian populations for many species around the globe.

The caddisflies (order Trichoptera) are a group of insects with aquatic larvae and terrestrial adults. There are approximately 14,500 described species, most of which can be divided into the suborders Integripalpia and Annulipalpia on the basis of the adult mouthparts. Integripalpian larvae construct a portable casing to protect themselves as they move around looking for food, while annulipalpian larvae make themselves a fixed retreat in which they remain, waiting for food to come to them. The affinities of the small third suborder Spicipalpia are unclear, and molecular analysis suggests it may not be monophyletic. Also called sedge-flies or rail-flies, the adults are small moth-like insects with two pairs of hairy membranous wings. They are closely related to the Lepidoptera (moths and butterflies) which have scales on their wings; the two orders together form the superorder Amphiesmenoptera.

The aquatic larvae are found in a wide variety of habitats such as streams, rivers, lakes, ponds, spring seeps and temporary waters (vernal pools), and even the ocean. The larvae of many species use silk to make protective cases, which are often strengthened with gravel, sand, twigs, bitten-off pieces of plants, or other debris. The larvae exhibit various feeding strategies, with different species being predators, leaf shredders, algal grazers, or collectors of particles from the water column and benthos. Most adults have short lives during which they do not feed.

The dinoflagellates (from Ancient Greek δῖνος (dînos) 'whirling' and Latin flagellum 'whip, scourge'), also called dinophytes, are a monophyletic group of single-celled eukaryotes constituting the phylum Dinoflagellata and are usually considered protists. Dinoflagellates are mostly marine plankton, but they are also common in freshwater habitats. Their populations vary with sea surface temperature, salinity, and depth. Many dinoflagellates are photosynthetic, but a large fraction of these are in fact mixotrophic, combining photosynthesis with ingestion of prey (phagotrophy and myzocytosis).

In terms of number of species, dinoflagellates are one of the largest groups of marine eukaryotes, although substantially smaller than diatoms. Some species are endosymbionts of marine animals and play an important part in the biology of coral reefs. Other dinoflagellates are unpigmented predators on other protozoa, and a few forms are parasitic (for example, Oodinium and Pfiesteria). Some dinoflagellates produce resting stages, called dinoflagellate cysts or dinocysts, as part of their lifecycles; this occurs in 84 of the 350 described freshwater species and a little more than 10% of the known marine species. Dinoflagellates are alveolates possessing two flagella, the ancestral condition of bikonts.

Platyhelminthes (from Ancient Greek πλατύ platy 'flat' and ἕλμινς helmins 'parasitic worm') is a phylum of relatively simple bilaterian, unsegmented, soft-bodied invertebrates commonly called flatworms or flat worms. Being acoelomates (having no body cavity), and having no specialised circulatory and respiratory organs, they are restricted to having flattened shapes that allow oxygen and nutrients to pass through their bodies by diffusion. The digestive cavity has only one opening for both ingestion (intake of nutrients) and egestion (removal of undigested wastes); as a result, the food can not be processed continuously.

In traditional medicinal texts, Platyhelminthes are divided into Turbellaria, which are mostly non-parasitic animals such as planarians, and three entirely parasitic groups: Cestoda, Trematoda and Monogenea; however, since the turbellarians have since been proven not to be monophyletic, this classification is now deprecated. Free-living flatworms are mostly predators, and live in water or in shaded, humid terrestrial environments, such as leaf litter. Cestodes (tapeworms) and trematodes (flukes) have complex life-cycles, with mature stages that live as parasites in the digestive systems of fish or land vertebrates, and intermediate stages that infest secondary hosts. The eggs of trematodes are excreted from their main hosts, whereas adult cestodes generate vast numbers of hermaphroditic, segment-like proglottids that detach when mature, are excreted, and then release eggs. Unlike the other parasitic groups, the monogeneans are external parasites infesting aquatic animals, and their larvae metamorphose into the adult form after attaching to a suitable host.

The Archaeplastida (or kingdom Plantae sensu lato "in a broad sense"; pronounced /ɑːrkɪˈplæstɪdə/) are a major group of eukaryotes, comprising the photoautotrophic red algae (Rhodophyta), green algae, land plants, and the minor group glaucophytes. It also includes the non-photosynthetic lineage Rhodelphidia, a predatorial (eukaryotrophic) flagellate that is sister to the Rhodophyta, and probably the microscopic picozoans. The Archaeplastida have chloroplasts that are surrounded by two membranes, suggesting that they were acquired directly through a single endosymbiosis event by phagocytosis of a cyanobacterium. All other groups which have chloroplasts, besides the amoeboid genus Paulinella, have chloroplasts surrounded by three or four membranes, suggesting they were acquired secondarily from red or green algae. Unlike red and green algae, glaucophytes have never been involved in secondary endosymbiosis events.

The cells of the Archaeplastida typically lack centrioles and have mitochondria with flat cristae. They usually have a cell wall that contains cellulose, and food is stored in the form of starch. However, these characteristics are also shared with other eukaryotes. The main evidence that the Archaeplastida form a monophyletic group comes from genetic studies, which indicate their plastids probably had a single origin. This evidence is disputed. Based on the evidence to date, it is not possible to confirm or refute alternative evolutionary scenarios to a single primary endosymbiosis. Photosynthetic organisms with plastids of different origin (such as brown algae) do not belong to the Archaeplastida.

A supergroup or super-group, in systematics, is a large group of organisms that share one common ancestor and have important defining characteristics. It is an informal, mostly arbitrary rank in biological taxonomy that is often greater than phylum or kingdom, although some supergroups are also treated as phyla.

Amoebozoa is a major taxonomic group containing about 2,400 described species of amoeboid protists, often possessing blunt, fingerlike, lobose pseudopods and tubular mitochondrial cristae. In traditional classification schemes, Amoebozoa is usually ranked as a phylum within either the kingdom Protista or the kingdom Protozoa. In the classification favored by the International Society of Protistologists, it is retained as an unranked "supergroup" within Eukaryota. Molecular genetic analysis supports Amoebozoa as a monophyletic clade. Modern studies of eukaryotic phylogenetic trees identify it as the sister group to Opisthokonta, another major clade which contains both fungi and animals as well as several other clades comprising some 300 species of unicellular eukaryotes. Amoebozoa and Opisthokonta are sometimes grouped together in a high-level taxon, named Amorphea.Amoebozoa includes many of the best-known amoeboid organisms, such as Chaos, Entamoeba, Pelomyxa and the genus Amoeba itself. Species of Amoebozoa may be either shelled (testate) or naked, and cells may possess flagella. Free-living species are common in both salt and freshwater as well as soil, moss and leaf litter. Some live as parasites or symbionts of other organisms, and some are known to cause disease in humans and other organisms.

While the majority of amoebozoan species are unicellular, the group also includes several clades of slime molds, which have a macroscopic, multicellular stage of life during which individual amoeboid cells remain together after multiple cell division to form a macroscopic plasmodium or, in cellular slime molds, aggregate to form one.

The Ascomycota are a phylum in the kingdom Fungi that, together with the Basidiomycota, form the subkingdom Dikarya. Members of Ascomycota are commonly known as the sac fungi or ascomycetes. It is the largest phylum of Fungi, with over 64,000 species. The defining feature of this fungal group is the ascus (from Ancient Greek ἀσκός (askós) 'sac, wineskin'), a microscopic sexual structure in which nonmotile spores, called ascospores, are formed. However, some species of Ascomycota are asexual and thus do not form asci or ascospores. Familiar examples of sac fungi include morels, truffles, brewers' and bakers' yeast, dead man's fingers, and cup fungi. The fungal symbionts in the majority of lichens (loosely termed "ascolichens") such as Cladonia belong to the Ascomycota.

Ascomycota are a monophyletic group (containing all of the descendants of a common ancestor). Previously placed in the Basidiomycota along with asexual species from other fungal taxa, asexual (or anamorphic) ascomycetes are now identified and classified based on morphological or physiological similarities to ascus-bearing taxa, and by phylogenetic analyses of DNA sequences.

Satureja is a genus of aromatic plants of the family Lamiaceae, related to rosemary and thyme. It is native to southern and southeastern Europe, North Africa, the Middle East, and Central Asia. Historically, Satureja was defined broadly and many species of the subtribe Menthinae from throughout the world were included in it. In the modern cladistic era of botany, Satureja was redefined to a narrower monophyletic genus whose species are all native to Eurasia. Several species are cultivated as culinary herbs called savory, and they have become established in the wild in a few places.

The Pinaceae, or pine family, are conifer trees or shrubs, including many of the well-known conifers of commercial importance such as cedars, firs, hemlocks, larches, pines and spruces. The family is included in the order Pinales, formerly known as Coniferales. Pinaceae have distinctive cones with woody scales bearing typically two ovules, and are supported as monophyletic by both morphological trait and genetic analysis. They are the largest extant conifer family in species diversity, with between 220 and 250 species (depending on taxonomic opinion) in 11 genera, and the second-largest (after Cupressaceae) in geographical range, found in most of the Northern Hemisphere, with the majority of the species in temperate climates, but ranging from subarctic to tropical. The family often forms the dominant component of boreal, coastal, and montane forests. One species, Pinus merkusii, grows just south of the equator in Southeast Asia. Major centres of diversity are found in the mountains of southwest China, Mexico, central Japan, and California.

Adapiformes is a group of early primates. Adapiforms radiated throughout much of the northern continental mass (now Europe, Asia and North America), reaching as far south as northern Africa and tropical Asia. They existed from the Eocene to the Miocene epoch. Some adapiforms resembled living lemurs.

Adapiforms are known from the fossil record only, and it is unclear whether they form a monophyletic or paraphyletic group. When assumed to be a clade, they are usually grouped under the "wet-nosed" taxon Strepsirrhini, which would make them more closely related to the lemurs and less so to the "dry-nosed" Haplorhini taxon that includes monkeys and apes.