Molecular phylogeny in the context of "Ultrastructural"

An oak is a hardwood tree or shrub in the genus Quercus of the beech family. They have spirally arranged leaves, often with lobed edges, and a nut called an acorn, borne within a cup. The genus is widely distributed in the Northern Hemisphere, with some 500 species, both deciduous and evergreen. Fossil oaks date back to the Middle Eocene. Molecular phylogeny shows that the genus is divided into Old World and New World clades, but many oak species hybridise freely, making the genus's history difficult to resolve.

Ecologically, oaks are keystone species in habitats from Mediterranean semi-desert to subtropical rainforest. They live in association with many kinds of fungi including truffles. Oaks support more than 950 species of caterpillar, many kinds of gall wasp which form distinctive galls (roundish woody lumps such as the oak apple), and a large number of pests and diseases. Oak leaves and acorns contain enough tannin to be toxic to cattle, but pigs are able to digest them safely. Oak timber is strong and hard, and has found many uses in construction and furniture-making. The bark was traditionally used for tanning leather. Wine barrels are made of oak; these are used for aging alcoholic beverages such as sherry and whisky, giving them a range of flavours, colours, and aromas. The spongy bark of the cork oak is used to make traditional wine bottle corks. Almost a third of oak species are threatened with extinction due to climate change, invasive pests, and habitat loss.

Chlamydomonas (/ˌklæmɪˈdɒmənəs, -dəˈmoʊ-/ KLAM-ih-DOM-ə-nəs, -⁠də-MOH-) is a genus of green algae consisting of about 150 species of unicellular flagellates, found in stagnant water and on damp soil, in freshwater, seawater, and even in snow as "snow algae". Chlamydomonas is used as a model organism for molecular biology, especially studies of flagellar motility and chloroplast dynamics, biogenesis, and genetics. One of the many striking features of Chlamydomonas is that it contains ion channels (channelrhodopsins) that are directly activated by light. Some regulatory systems of Chlamydomonas are more complex than their homologs in Gymnosperms, with evolutionarily related regulatory proteins being larger and containing additional domains.

Molecular phylogeny studies indicated that the traditional genus Chlamydomonas as defined using morphological data, was polyphyletic within Volvocales. Many species were subsequently reclassified (e.g., Oogamochlamys, Lobochlamys), and many other "Chlamydomonas" s.l. lineages are still to be reclassified.

Lepidostromatales is an order of fungi in the class Agaricomycetes. It is the only known order of basidiomycete fungi composed entirely of lichenized members. Morphologically, the fruiting bodies of all species are clavarioid. Six species are known, five of which were described within the span of 2007–2013. Due to its morphological similarity to the genus Multiclavula, its isolated phylogenetic position (distinct from all other orders based on molecular data) was not understood until quite recently. The photobionts that have been found in association with members of this group are not known to associate with any other types of lichenized fungi.

The Muroidea are a large superfamily of rodents, including mice, rats, voles, hamsters, lemmings, gerbils, and many other relatives. Although the Muroidea originated in Eurasia, they occupy a vast variety of habitats on every continent except Antarctica. Some authorities have placed all members of this group into a single family, Muridae, due to difficulties in determining how the subfamilies are related to one another. Many of the families within the Muroidea superfamily have more variations between the families than between the different clades. A possible explanation for the variations in rodents is because of the location of these rodents; these changes could have been due to radiation or the overall environment they migrated to or originated in. The following taxonomy is based on recent well-supported molecular phylogenies.

The muroids are classified in six families, 19 subfamilies, around 280 genera, and at least 1,750 species.