Phylogenetics in the context of Symplesiomorphy

Biodiversity is the variability of life on Earth. It can be measured on various levels, for example, genetic variability, species diversity, ecosystem diversity and phylogenetic diversity. Diversity is not distributed evenly on Earth—it is greater in the tropics as a result of the warm climate and high primary productivity in the region near the equator. Tropical forest ecosystems cover less than one-fifth of Earth's terrestrial area and contain about 50% of the world's species. There are latitudinal gradients in species diversity for both marine and terrestrial taxa.

Since life began on Earth, six major mass extinctions and several minor events have led to large and sudden drops in biodiversity. The Phanerozoic aeon (the last 540 million years) marked a rapid growth in biodiversity via the Cambrian explosion. In this period, the majority of multicellular phyla first appeared. The next 400 million years included repeated, massive biodiversity losses. Those events have been classified as mass extinction events. In the Carboniferous, rainforest collapse may have led to a great loss of plant and animal life. The Permian–Triassic extinction event, 251 million years ago, was the worst; vertebrate recovery took 30 million years.

Charles Robert Darwin (/ˈdɑːrwɪn/ DAR-win; 12 February 1809 – 19 April 1882) was an English naturalist, geologist, and biologist, widely known for his contributions to evolutionary biology. His proposition that all species of life have descended from a common ancestor is now generally accepted and considered a fundamental scientific concept. In a joint presentation with Alfred Russel Wallace, he introduced his scientific theory that this branching pattern of evolution resulted from a process he called natural selection, in which the struggle for existence has a similar effect to the artificial selection involved in selective breeding. Darwin has been described as one of the most influential figures in human history and was honoured by burial in Westminster Abbey.

Darwin's early interest in nature led him to neglect his medical education at the University of Edinburgh; instead, he helped Grant to investigate marine invertebrates. His studies at the University of Cambridge's Christ's College from 1828 to 1831 encouraged his passion for natural science. However, it was his five-year voyage on HMS Beagle from 1831 to 1836 that truly established Darwin as an eminent geologist. The observations and theories he developed during his voyage supported Charles Lyell's concept of gradual geological change. Publication of his journal of the voyage made Darwin famous as a popular author. His first scientific work was The Structure and Distribution of Coral Reefs (1842). Along with his work on barnacles, it won him the Royal Medal in 1853.

Eumetazoa (from Ancient Greek εὖ (eû) 'well' μετά (metá) 'after' and ζῷον (zôion) 'animal'), also known as Epitheliozoa or Histozoa, is a proposed basal animal subkingdom as a sister group of Porifera (sponges). The basal eumetazoan clades are the Ctenophora and the ParaHoxozoa. Placozoa is now also seen as a eumetazoan in the ParaHoxozoa. The competing hypothesis is the Myriazoa clade. The subkingdom Parazoa and Agnotozoa are the other taxa, and agnotozoa may be fake or even nonexistent at studies. Parazoa or Agnotozoa are a main sister group to eumetazoans, forming clade Blastozoa/Diploblastozoa. Alternatively,Parazoa was considered as a sister group to Agnotozoa (now considered polyphyletic).Several other extinct or obscure life forms, such as Iotuba and Thectardis, appear to have emerged in the group. Characteristics of eumetazoans include true tissues organized into germ layers, the presence of neurons and muscles, and an embryo that goes through a gastrula stage.

Some phylogenists once speculated the sponges and eumetazoans evolved separately from different single-celled organisms, which would have meant that the animal kingdom does not form a clade (a complete grouping of all organisms descended from a common ancestor). However, genetic studies and some morphological characteristics, like the common presence of choanocytes, now unanimously support a common origin.

A fish is an aquatic, anamniotic, gill-bearing vertebrate animal with swimming fins and a hard skull, but lacking limbs with digits. Fish can be grouped into the more basal jawless fish and the more common jawed fish, the latter including all living cartilaginous and bony fish, as well as the extinct placoderms and acanthodians. In a break from the long tradition of grouping all fish into a single class (Pisces), modern phylogenetics views fish as a paraphyletic group which includes all vertebrates except tetrapods. In English, the plural of "fish" is fish when referring to individuals and fishes when referring to species.

Most fish are cold-blooded, their body temperature varying with the surrounding water, though some large, active swimmers like the white shark and tuna can maintain a higher core temperature. Many fish can communicate acoustically with each other, such as during courtship displays. The study of fish is known as ichthyology.

Zoogeography is the branch of the science of biogeography that is concerned with geographic distribution (present and past) of animal species.

As a multifaceted field of study, zoogeography incorporates methods of molecular biology, genetics, morphology, phylogenetics, and Geographic Information Systems (GIS) to delineate evolutionary events within defined regions of study around the globe. As proposed by Alfred Russel Wallace, known as the father of zoogeography, phylogenetic affinities can be quantified among zoogeographic regions, further elucidating the phenomena surrounding geographic distributions of organisms and explaining evolutionary relationships of taxa.

Plankton are organisms that drift in water (or air) but are unable to actively propel themselves against currents (or wind). Marine plankton include drifting organisms that inhabit the saltwater of oceans and the brackish waters of estuaries. Freshwater plankton are similar to marine plankton, but are found in lakes and rivers. An individual plankton organism in the plankton is called a plankter. In the ocean plankton provide a crucial source of food, particularly for larger filter-feeding animals, such as bivalves, sponges, forage fish and baleen whales.

Plankton includes organisms from species across all the major biological kingdoms, ranging in size from the microscopic (such as bacteria, archaea, protozoa and microscopic algae and fungi) to larger organisms (such as jellyfish and ctenophores). This is because plankton are defined by their ecological niche and level of motility rather than by any phylogenetic or taxonomic classification. The plankton category differentiates organisms from those that can swim against a current, called nekton, and those that live on the deep sea floor, called benthos. Organisms that float on or near the water's surface are called neuston. Neuston that drift as water currents or wind take them, and lack the swimming ability to counter this, form a special subgroup of plankton. Mostly plankton just drift where currents take them, though some, like jellyfish, swim slowly but not fast enough to generally overcome the influence of currents.

Human anatomy (gr. ἀνατομία, "dissection", from ἀνά, "up", and τέμνειν, "cut") is primarily the scientific study of the morphology of the human body. Anatomy is subdivided into gross anatomy and microscopic anatomy. Gross anatomy (also called macroscopic anatomy, topographical anatomy, regional anatomy, or anthropotomy) is the study of anatomical structures that can be seen by the naked eye. Microscopic anatomy is the study of minute anatomical structures assisted with microscopes, which includes histology (the study of the organization of tissues), and cytology (the study of cells). Anatomy, human physiology (the study of function), and biochemistry (the study of the chemistry of living structures) are complementary basic medical sciences that are generally together (or in tandem) to students studying medical sciences.

In some of its facets human anatomy is closely related to embryology, comparative anatomy and comparative embryology, through common roots in evolution; for example, much of the human body maintains the ancient segmental pattern that is present in all vertebrates with basic units being repeated, which is particularly obvious in the vertebral column and in the ribcage, and can be traced from very early embryos.

Guinea fowl (/ˈɡɪnifaʊl/) are birds of the family Numididae in the order Galliformes. They are endemic to Africa and rank among the oldest of the gallinaceous birds. Phylogenetically, they branched off from the core Galliformes after the Cracidae (chachalacas, guans, and curassows) and before the Odontophoridae (New World quail). An Eocene fossil lineage Telecrex has been associated with guinea fowl; Telecrex inhabited Mongolia, and may have given rise to the oldest of the true phasianids, such as blood pheasants and eared pheasants, which evolved into high-altitude, montane-adapted species with the rise of the Tibetan Plateau. While modern guinea fowl species are endemic to Africa, the helmeted guinea fowl has been introduced as a domesticated bird widely elsewhere.

Dinosaurs are a diverse group of reptiles of the clade Dinosauria. They first appeared during the Triassic period, between 243 and 233.23 million years ago (mya), although the exact origin and timing of the evolution of dinosaurs is a subject of active research. They became the dominant terrestrial vertebrates after the Triassic–Jurassic extinction event 201.3 mya and their dominance continued throughout the Jurassic and Cretaceous periods. The fossil record shows that birds are feathered dinosaurs, having evolved from earlier theropods during the Late Jurassic epoch, and are the only dinosaur lineage known to have survived the Cretaceous–Paleogene extinction event approximately 66 mya. Dinosaurs can therefore be divided into avian dinosaurs—birds—and the extinct non-avian dinosaurs, which are all dinosaurs other than birds.

Dinosaurs are varied from taxonomic, morphological and ecological standpoints. Birds, at over 11,000 living species, are among the most diverse groups of vertebrates. Using fossil evidence, paleontologists have identified over 900 distinct genera and more than 1,000 different species of non-avian dinosaurs. Dinosaurs are represented on every continent by both extant species (birds) and fossil remains. Through most of the 20th century, before birds were recognized as dinosaurs, most of the scientific community believed dinosaurs to have been sluggish and cold-blooded. Most research conducted since the 1970s, however, has indicated that dinosaurs were active animals with elevated metabolisms and numerous adaptations for social interaction. Some were herbivorous, others carnivorous. Evidence suggests that all dinosaurs were egg-laying, and that nest-building was a trait shared by many dinosaurs, both avian and non-avian.

A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time. In other words, it is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. In evolutionary biology, all life on Earth is theoretically part of a single phylogenetic tree, indicating common ancestry. Phylogenetics is the study of phylogenetic trees. The main challenge is to find a phylogenetic tree representing optimal evolutionary ancestry between a set of species or taxa. Computational phylogenetics (also phylogeny inference) focuses on the algorithms involved in finding optimal phylogenetic tree in the phylogenetic landscape.

Phylogenetic trees may be rooted or unrooted. In a rooted phylogenetic tree, each node with descendants represents the inferred most recent common ancestor of those descendants, and the edge lengths in some trees may be interpreted as time estimates. Each node is called a taxonomic unit. Internal nodes are generally called hypothetical taxonomic units, as they cannot be directly observed. Trees are useful in fields of biology such as bioinformatics, systematics, and phylogenetics. Unrooted trees illustrate only the relatedness of the leaf nodes and do not require the ancestral root to be known or inferred.

In biology, the taxon (back-formation from taxonomy; pl.: taxa) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is usually known by a particular name and given a particular ranking, especially if and when it is accepted or becomes established. It is very common, however, for taxonomists to remain at odds over what belongs to a taxon and the criteria used for inclusion, especially in the context of rank-based ("Linnaean") nomenclature (much less so under phylogenetic nomenclature). If a taxon is given a formal scientific name, its use is then governed by one of the nomenclature codes specifying which scientific name is correct for a particular grouping.

Initial attempts at classifying and ordering organisms (plants and animals) were presumably set forth in prehistoric times by hunter-gatherers, as suggested by the fairly sophisticated folk taxonomies. Much later, Aristotle and, later still, European scientists, like Magnol, Tournefort and Carl Linnaeus's system in Systema Naturae, 10th edition (1758),, as well as an unpublished work by Bernard and Antoine Laurent de Jussieu, contributed to this field. The idea of a unit-based system of biological classification was first made widely available in 1805 in the introduction to Jean-Baptiste Lamarck's Flore françoise, and Augustin Pyramus de Candolle's Principes élémentaires de botanique. Lamarck set out a system for the "natural classification" of plants. Since then, systematists continue to construct accurate classifications encompassing the diversity of life; today, a "good" or "useful" taxon is commonly taken to be one that reflects evolutionary relationships.

Ornithology, from Ancient Greek ὄρνις (órnis), meaning "bird", and λόγος (lógos), meaning "study", is a branch of zoology dedicated to the study of birds. Several aspects of ornithology differ from related disciplines, due partly to the high visibility and the aesthetic appeal of birds. It has also been an area with a large contribution made by amateurs in terms of time, resources, and financial support. Studies on birds have helped develop key concepts in biology including evolution, behaviour and ecology such as the definition of species, the process of speciation, instinct, learning, ecological niches, guilds, insular biogeography, phylogeography, and conservation.

While early ornithology was principally concerned with descriptions and distributions of species, ornithologists today seek answers to very specific questions, often using birds as models to test hypotheses or predictions based on theories. Most modern biological theories apply across life forms, and the number of scientists who identify themselves as "ornithologists" has therefore declined. A wide range of tools and techniques are used in ornithology, both inside the laboratory and out in the field, and innovations are constantly made. Most biologists who recognise themselves as "ornithologists" study specific biology research areas, such as anatomy, physiology, taxonomy (phylogenetics), ecology, or behaviour.

The evolution of birds began in the Jurassic Period, with the earliest birds derived from a clade of theropod dinosaurs named Paraves. Birds are categorized as a biological class, Aves. For more than a century, the small theropod dinosaur Archaeopteryx lithographica from the Late Jurassic period was considered to have been the earliest bird. Modern phylogenies place birds in the dinosaur clade Theropoda. According to the current consensus, Aves and a sister group, the order Crocodilia, together are the sole living members of an unranked reptile clade, the Archosauria. Four distinct lineages of bird survived the Cretaceous–Paleogene extinction event 66 million years ago, giving rise to ostriches and relatives (Palaeognathae), waterfowl (Anseriformes), ground-living fowl (Galliformes), and "modern birds" (Neoaves).

Phylogenetically, Aves is usually defined as all descendants of the most recent common ancestor of a specific modern bird species (such as the house sparrow, Passer domesticus), and either Archaeopteryx, or some prehistoric species closer to Neornithes (to avoid the problems caused by the unclear relationships of Archaeopteryx to other theropods). If the latter classification is used then the larger group is termed Avialae. Currently, the relationship between non-avian dinosaurs, Archaeopteryx, and modern birds is still under debate.

In biology, a phylum (/ˈfaɪləm/; pl.: phyla) is a level of classification, or taxonomic rank, that is below kingdom and above class. Traditionally, in botany the term division has been used instead of phylum, although the International Code of Nomenclature for algae, fungi, and plants accepts the terms as equivalent. Depending on definitions, the animal kingdom Animalia contains about 31 phyla, the plant kingdom Plantae contains about 14 phyla, and the fungus kingdom Fungi contains about eight phyla. Current research in phylogenetics is uncovering the relationships among phyla within larger clades like Ecdysozoa and Embryophyta.

Molecular evolution describes how inherited DNA and/or RNA change over evolutionary time, and the consequences of this for proteins and other components of cells and organisms. Molecular evolution is the basis of phylogenetic approaches to describing the tree of life. Molecular evolution overlaps with population genetics, especially on shorter timescales. Topics in molecular evolution include the origins of new genes, the genetic nature of complex traits, the genetic basis of adaptation and speciation, the evolution of development, and patterns and processes underlying genomic changes during evolution.