Genetic divergence in the context of Phenotype

The Silurian-Devonian Terrestrial Revolution, also known as the Devonian Plant Explosion (DePE) and the Devonian explosion, was a period of rapid colonization, diversification and radiation of land plants (particularly vascular plants) and fungi (especially dikaryans) on dry lands that occurred 428 to 359 million years ago (Mya) during the Silurian and Devonian periods, with the most critical phase occurring during the Late Silurian and Early Devonian.

This diversification of terrestrial photosynthetic florae had vast impacts on the biotic composition of the Earth's surface, especially upon the Earth's atmosphere by oxygenation and carbon fixation. Their roots also eroded into the rocks, creating a layer of water-holding and mineral/organic matter-rich soil on top of Earth's crust known as the pedosphere, and significantly altering the chemistry of Earth's lithosphere and hydrosphere. The floral activities following the Silurian-Devonian plant revolution also exerted significant influences on changes in the water cycle and global climate, as well as driving the biosphere by creating diverse layers of vegetations that provide both sustenance and refuge for both upland and wetland habitats, paving the way for all terrestrial and aquatic biomes that would follow.

A mammal (from Latin mamma 'breast') is a vertebrate animal of the class Mammalia (/məˈmeɪli.ə/). Mammals are characterised by the presence of milk-producing mammary glands for feeding their young, a broad neocortex region of the brain, fur or hair, and three middle ear bones. These characteristics distinguish them from reptiles and birds, from which their ancestors diverged in the Carboniferous Period over 300 million years ago. Around 6,640 extant species of mammals have been described and divided into 27 orders. The study of mammals is called mammalogy.

The largest orders of mammals, by number of species, are the rodents, bats, and eulipotyphlans (including hedgehogs, moles and shrews). The next three are the primates (including humans, monkeys and lemurs), the even-toed ungulates (including pigs, bovids and whales), and the Carnivora (including cats, dogs, and seals).

Purported remains of Paleolithic dogs have been reported from several European archaeological sites dating to over 30,000 years ago. Their status as domesticated is highly controversial, with some authors suggesting them to be the ancestors of the domestic dog or an extinct, morphologically and genetically divergent wolf population.

The red panda (Ailurus fulgens), also known as the lesser panda, is a small mammal native to the eastern Himalayas and southwestern China. It has dense reddish-brown fur with a black belly and legs, white-lined ears, a mostly white muzzle and a ringed tail. Its head-to-body length is 51–63.5 cm (20.1–25.0 in) with a 28–48.5 cm (11.0–19.1 in) tail, and it weighs between 3.2 and 15 kg (7.1 and 33.1 lb). It is well adapted to climbing due to its flexible joints and curved semi-retractile claws.

The red panda was formally described in 1825. The two recognised subspecies, the Himalayan and the Chinese red panda, genetically diverged about 250,000 years ago. The red panda's place on the evolutionary tree has been debated, but modern genetic evidence places it in close affinity with raccoons, weasels, and skunks. It is not closely related to the giant panda, which is a bear, though both possess elongated wrist bones or "false thumbs" used for grasping bamboo. The evolutionary lineage of the red panda (Ailuridae) stretches back around 25 to 18 million years ago, as indicated by extinct fossil relatives found in Eurasia and North America.

The domestication of the dog was the process which led to the domestic dog. This included the dog's genetic divergence from the wolf, its domestication, and the emergence of the first dogs. Genetic studies suggest that all ancient and modern dogs share a common ancestry, descending from an ancient, now-extinct wolf population – or closely related wolf populations – which was distinct from the modern wolf lineage. The dog's similarity to the grey wolf is the result of substantial dog-into-wolf gene flow, with the modern grey wolf being the dog's nearest living relative. An extinct Late Pleistocene wolf may have been the ancestor of the dog.

The dog is a wolf-like canid. The genetic divergence between the dog's ancestor and modern wolves occurred between 20,000 and 40,000 years ago, just before or during the Last Glacial Maximum (20,000–27,000 years ago). This timespan represents the upper time-limit for the commencement of domestication because it is the time of divergence but not the time of domestication, which occurred later.

The Cretaceous Terrestrial Revolution (abbreviated KTR), also known as the Angiosperm Terrestrial Revolution (ATR) by authors who consider it to have lasted into the Paleogene, describes the intense floral diversification of flowering plants (angiosperms) and the coevolution of pollinating insects (especially anthophilans and lepidopterans), as well as the subsequent faunal radiation of various frugivorous, nectarivorous and insectivorous terrestrial animals then at the lower food web levels such as mammals, avialans (early birds and close relatives), squamate reptiles (lizards and snakes), lissamphibians (especially frogs) and web-spinning spiders, during the Cretaceous period.

After the K-Pg extinction event devastated the Mesozoic terrestrial ecosystems and wiped out nearly all animals weighing more than 25 kg (55 lb), the survivors among these smaller animals that thrived during the KTR recovered first to reoccupy the ecological niches vacated by the extinction of non-avian dinosaurs and pterosaurs, and therefore became the dominant clades of the Cenozoic terrestrial faunas. Flowering plants also quickly became the mainstream florae during the Cenozoic, replacing the previously more prevalent gymnosperms and ferns.

The Sirenia (/saɪˈriːniə/ sy-REE-nee-ə), commonly referred to as sea cows or sirenians, are an order of fully aquatic, herbivorous mammals that inhabit swamps, rivers, estuaries, marine wetlands, and coastal marine waters. The extant Sirenia comprise two distinct families: Dugongidae (the dugong and the now extinct Steller's sea cow) and Trichechidae (manatees, namely the Amazonian manatee, West Indian manatee, and West African manatee) with a total of four species. The Protosirenidae (Eocene sirenians) and Prorastomidae (terrestrial sirenians) families are extinct. Sirenians are classified in the clade Paenungulata, alongside the elephants and the hyraxes, and evolved in the Eocene 50 million years ago (mya). The Dugongidae diverged from the Trichechidae in the late Eocene or early Oligocene (30–35 mya).

Sirenians grow to between 2.5 and 4 metres (8.2 and 13.1 feet) in length and 1,500 kilograms (3,300 pounds) in weight. The recently extinct Steller's sea cow was the largest known sirenian to have lived, reaching lengths of 10 metres (33 feet) and weights of 5 to 10 tonnes (5.5 to 11.0 short tons).

The molecular clock is a figurative term for a technique that uses the mutation rate of biomolecules to deduce the time in prehistory when two or more life forms diverged. The biomolecular data used for such calculations are usually nucleotide sequences for DNA, RNA, or amino acid sequences for proteins.

In parapatric speciation, two subpopulations of a species evolve reproductive isolation from one another while continuing to exchange genes. This mode of speciation has three distinguishing characteristics: 1) mating occurs non-randomly, 2) gene flow occurs unequally, and 3) populations exist in either continuous or discontinuous geographic ranges. This distribution pattern may be the result of unequal dispersal, incomplete geographical barriers, or divergent expressions of behavior, among other things. Parapatric speciation predicts that hybrid zones will often exist at the junction between the two populations.

In biogeography, the terms parapatric and parapatry are often used to describe the relationship between organisms whose ranges do not significantly overlap but are immediately adjacent to each other; they do not occur together except in a narrow contact zone. Parapatry is a geographical distribution opposed to sympatry (same area) and allopatry or peripatry (two similar cases of distinct areas).

The island of Borneo is located on the Sunda Shelf, which is an extensive region in Southeast Asia of immense importance in terms of biodiversity, biogeography and phylogeography of fauna and flora that had attracted Alfred Russel Wallace and other biologists from all over the world.

The previous climatic oscillation and sea level changes leading to contraction and expansion of the tropical rain contributed to the extinction and genetic divergence of species in the region. Harrison (1958) was the first to discover of intermittent human habitation about 49,000 years ago in the Niah Cave National Park. Baker et al.(2007) unravelled the complexities of the late Pleistocene to Holocene habitation of the Niah Cave.

Panthera spelaea, commonly known as the cave lion (or less commonly as the steppe lion), is an extinct Panthera species that was native to Eurasia and northwest North America during the Pleistocene epoch. Genetic analysis of ancient DNA has revealed that while closely related, it was a distinct species genetically isolated from the modern lion (Panthera leo), with the genetic divergence between the two species estimated at around 500,000 years ago.

The earliest fossils of the P. spelaea lineage (either regarded as the separate species Panthera fossilis or the subspecies P. spelaea fossilis) in Eurasia date to around 700,000 years ago (with possible late Early Pleistocene records). It is closely related and probably ancestral to the American lion (Panthera atrox). The species ranged from Western Europe to eastern Beringia in North America, and was a prominent member of the mammoth steppe fauna, and an important apex predator across its range along with other large carnivores like cave hyenas, which cave lions came into conflict with.

A mongoose is a small terrestrial carnivorous mammal belonging to the family Herpestidae. This family has two subfamilies, the Herpestinae and the Mungotinae. The Herpestinae comprises 23 living species that are native to southern Europe, Africa and Asia, whereas the Mungotinae comprises 11 species native to Africa. The Herpestidae originated about 21.8 ± 3.6 million years ago in the Early Miocene and genetically diverged into two main lineages between 19.1 and 18.5 ± 3.5 million years ago. There is a large introduced population on the islands of Hawaii. Mongoose diets are varied but consist of mainly insects, hatchlings, reptiles and birds.

Horseshoe bats are bats in the family Rhinolophidae. In addition to the single living genus, Rhinolophus, which has about 106 species, the extinct genus Palaeonycteris has been recognized. Horseshoe bats are closely related to the Old World leaf-nosed bats, family Hipposideridae, which have sometimes been included in Rhinolophidae. The horseshoe bats are divided into six subgenera and many species groups. The most recent common ancestor of all horseshoe bats lived 34–40 million years ago, though it is unclear where the geographic roots of the family are, and attempts to determine its biogeography have been indecisive. Their taxonomy is complex, as genetic evidence shows the likely existence of many cryptic species, as well as species recognized as distinct that may have little genetic divergence from previously recognized taxa. They are found in the Old World, mostly in tropical or subtropical areas, including Africa, Asia, Europe, and Oceania.

Horseshoe bats are considered small or medium-sized microbats, weighing 4–28 g (0.14–0.99 oz), with forearm lengths of 30–75 mm (1.2–3.0 in) and combined lengths of head and body of 35–110 mm (1.4–4.3 in). The fur, long and smooth in most species, can be reddish-brown, blackish, or bright orange-red. They get their common name from their large nose-leafs, which are shaped like horseshoes. The nose-leafs aid in echolocation; horseshoe bats have highly sophisticated echolocation, using constant frequency calls at high-duty cycles to detect prey in areas of high environmental clutters. They hunt insects and spiders, swooping down on prey from a perch, or gleaning from foliage. Little is known about their mating systems, but at least one species is monogamous, while another is polygynous. Gestation is approximately seven weeks and one offspring is produced at a time. A typical lifespan is six or seven years, but one greater horseshoe bat lived more than thirty years.

During the Pleistocene, wolves were widely distributed across the Northern Hemisphere. Some Pleistocene wolves, such as Beringian wolves and those from Japan, exhibited large body size in comparison to modern gray wolf populations. Genetic analysis of the remains of Late Pleistocene wolves suggest that across their range populations of wolves maintained considerable gene flow between each other and thus there was limited genetic divergence between them. Modern wolves mostly draw their ancestry from some Siberian populations of Late Pleistocene gray wolves, which largely replaced other gray wolf populations after the Last Glacial Maximum.