Molecular clock

molecular clock hypothesismolecular datingmolecular clocks
Knowledge of approximately constant rate of molecular evolution in particular sets of lineages also facilitates establishing the dates of phylogenetic events, including those not documented by fossils, such as the divergence of living taxa and the formation of the phylogenetic tree. In these cases—especially over long stretches of time—the limitations of MCH (above) must be considered; such estimates may be off by 50% or more. Changing generation times (If the rate of new mutations depends at least partly on the number of generations rather than the number of years). Population size (Genetic drift is stronger in small populations, and so more mutations are effectively neutral).

Hybrid (biology)

hybridhybridshybridization
The European edible frog is a semi-permanent hybrid between pool frogs and marsh frogs; its population requires the continued presence of at least one of the parent species. Cave paintings indicate that the European bison is a natural hybrid of the aurochs and the steppe bison. Plant Hybridization is more commonplace compared to animal hybridization. Many crop species are hybrids, including notably the polyploid wheats: some have four sets of chromosomes (tetraploid) or six (hexaploid), while other wheat species have (like most eukaryotic organisms) two sets (diploid), so hybridization events likely involved the doubling of chromosome sets, causing immediate genetic isolation.

Homology (biology)

homologoushomologyorthologs
Two segments of DNA can have shared ancestry because of either a speciation event (orthologs) or a duplication event (paralogs). Homology among proteins or DNA is typically inferred from their sequence similarity. Significant similarity is strong evidence that two sequences are related by divergent evolution of a common ancestor. Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. Homologous sequences are orthologous if they are descended from the same ancestral sequence separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous.

Common descent

common ancestorcommon ancestryapical ancestor
Another important piece of evidence is from detailed phylogenetic trees (i.e., "genealogic trees" of species) mapping out the proposed divisions and common ancestors of all living species. In 2010, Douglas L. Theobald published a statistical analysis of available genetic data, mapping them to phylogenetic trees, that gave "strong quantitative support, by a formal test, for the unity of life." Traditionally, these trees have been built using morphological methods, such as appearance, embryology, etc. Recently, it has been possible to construct these trees using molecular data, based on similarities and differences between genetic and protein sequences.

Evolution

evolvedtheory of evolutionevolutionary theory
The importance of hybridisation in producing new species of animals is unclear, although cases have been seen in many types of animals, with the gray tree frog being a particularly well-studied example. Speciation has been observed multiple times under both controlled laboratory conditions (see laboratory experiments of speciation) and in nature. In sexually reproducing organisms, speciation results from reproductive isolation followed by genealogical divergence. There are four primary geographic modes of speciation. The most common in animals is allopatric speciation, which occurs in populations initially isolated geographically, such as by habitat fragmentation or migration.

On the Origin of Species

Origin of SpeciesThe Origin of SpeciesOn the Origin of Species by Means of Natural Selection
He now realised that the branching pattern of evolutionary divergence was explained by natural selection working constantly to improve adaptation. His thinking changed from the view that species formed in isolated populations only, as on islands, to an emphasis on speciation without isolation; that is, he saw increasing specialisation within large stable populations as continuously exploiting new ecological niches. He conducted empirical research focusing on difficulties with his theory.

Species

specificspecific namespecific epithet
The evolutionary process by which biological populations evolve to become distinct or reproductively isolated as species is called speciation. Charles Darwin was the first to describe the role of natural selection in speciation in his 1859 book The Origin of Species. Speciation depends on a measure of reproductive isolation, a reduced gene flow. This occurs most easily in allopatric speciation, where populations are separated geographically and can diverge gradually as mutations accumulate.

Natural selection

selectionselectiveselected
Speciation requires a degree of reproductive isolation—that is, a reduction in gene flow. However, it is intrinsic to the concept of a species that hybrids are selected against, opposing the evolution of reproductive isolation, a problem that was recognised by Darwin. The problem does not occur in allopatric speciation with geographically separated populations, which can diverge with different sets of mutations. E. B. Poulton realized in 1903 that reproductive isolation could evolve through divergence, if each lineage acquired a different, incompatible allele of the same gene.

Extinction

extinctspecies extinction
A 2018 report indicated that the phylogenetic diversity of 300 mammalian species erased during the human era since the Late Pleistocene would require 5 to 7 million years to recover. A dagger symbol placed next to the name of a species or other taxon normally indicates its status as extinct. A species is extinct when the last existing member dies. Extinction therefore becomes a certainty when there are no surviving individuals that can reproduce and create a new generation.

Hybrid zone

hybridizationoverlap in distributionzones of hybridization
Hybrid speciation. Introgression. Hybrizyme.

Cladogram

cladogramsphylogenetic treescladistic analysis
There are many other phylogenetic algorithms that treat data somewhat differently, and result in phylogenetic trees that look like cladograms but are not cladograms.

Gene

genesnumber of genesgene sequence
Additionally, any selection on a gene will cause its sequence to diverge at a different rate. Genes under stabilizing selection are constrained and so change more slowly whereas genes under directional selection change sequence more rapidly. The sequence differences between genes can be used for phylogenetic analyses to study how those genes have evolved and how the organisms they come from are related. The most common source of new genes in eukaryotic lineages is gene duplication, which creates copy number variation of an existing gene in the genome. The resulting genes (paralogs) may then diverge in sequence and in function. Sets of genes formed in this way compose a gene family.

Convergent evolution

convergentconvergenceanalogous
The opposite of convergence is divergent evolution, where related species evolve different traits. Convergent evolution is similar to parallel evolution, which occurs when two independent species evolve in the same direction and thus independently acquire similar characteristics; for instance, gliding frogs have evolved in parallel from multiple types of tree frog. Many instances of convergent evolution are known in plants, including the repeated development of C 4 photosynthesis, seed dispersal by fleshy fruits adapted to be eaten by animals, and carnivory.

Reproductive isolation

reproductively isolatedisolating mechanismsisolating mechanism
It has been demonstrated recently that Lhr has functionally diverged in D. simulans and will interact with Hmr which, in turn, has functionally diverged in D. melanogaster to cause the lethality of the male hybrids. Lhr is located in a heterochromatic region of the genome and its sequence has diverged between these two species in a manner consistent with the mechanisms of positive selection.

Vertebrate

Vertebratavertebratesvertebral
Most scientists working with vertebrates use a classification based purely on phylogeny, organized by their known evolutionary history and sometimes disregarding the conventional interpretations of their anatomy and physiology. In phylogenetic taxonomy, the relationships between animals are not typically divided into ranks, but illustrated as a nested "family tree" known as a phylogenetic tree. The one below is based on studies compiled by Philippe Janvier and others for the Tree of Life Web Project and Delsuc et al. The number of described vertebrate species are split evenly between tetrapods and fish.

Bioinformatics

bioinformaticbioinformaticiangenome browser
It is these intergenomic maps that make it possible to trace the evolutionary processes responsible for the divergence of two genomes. A multitude of evolutionary events acting at various organizational levels shape genome evolution. At the lowest level, point mutations affect individual nucleotides. At a higher level, large chromosomal segments undergo duplication, lateral transfer, inversion, transposition, deletion and insertion. Ultimately, whole genomes are involved in processes of hybridization, polyploidization and endosymbiosis, often leading to rapid speciation.

Parapatric speciation

parapatricparapatryat the very limits of the range
Quantitative speciation research Species populations that join, forming an ecotone can be interpreted as convincingly forming in parapatry if:. No evidence exists for a period of geographic separation between two closely related species. Different loci are not in agreement along the cline. Phylogenies including sister groups support different divergence times. An endemic species that exists within a specialized habitat next to its sister species that does not reside in the specialized habitat strongly suggests parapatric speciation. History of speciation. Evidence for speciation by reinforcement.

Gene flow

geneflowgenetic exchangemigration
"Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of HGT. Combining the simple coalescence model of cladogenesis with rare HGT events suggest there was no single last common ancestor that contained all of the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history and traces back to an individual molecule cenancestor. However, these molecular ancestors were likely to be present in different organisms at different times."

Computational phylogenetics

computational phylogeneticphylogenetic inferenceBayesian
While such an assumption may hold on a larger scale (bar horizontal gene transfer, see above), speciation is often much less orderly. Research since the cladistic method was introduced has shown that hybrid speciation, once thought rare, is in fact quite common, particularly in plants. Also paraphyletic speciation is common, making the assumption of a bifurcating pattern unsuitable, leading to phylogenetic networks rather than trees. Introgression can also move genes between otherwise distinct species and sometimes even genera, complicating phylogenetic analysis based on genes.

Most recent common ancestor

last common ancestorcommon ancestorrecent common ancestor
The project of a complete description of the phylogeny of biological species is dubbed the "Tree of Life". This involves time estimates of all known speciation events; for example, the MRCA of all Carnivora (i.e. the MRCA of "cats and dogs") is estimated to have lived of the order of 42 million years ago (Miacidae). The concept of the last common ancestor from the perspective of human evolution is described for a popular audience in The Ancestor's Tale by Richard Dawkins (2004).

Cladogenesis

splitcladogeneticsplitting
Note that with anagenesis the lineage in a phylogenetic tree does not split. To determine whether a speciation event is cladogenesis or anagenesis, researchers may use simulation, evidence from fossils, molecular evidence from the DNA of different living species, or modelling. It has however been debated whether the distinction between cladogenesis and anagenesis is necessary at all in evolutionary theory. Anagenesis. Evolutionary biology. Speciation.

Charles Darwin

DarwinDarwinianCharles
He began a major reassessment of his theory of species, and in November realised that divergence in the character of descendants could be explained by them becoming adapted to "diversified places in the economy of nature". By the start of 1856, Darwin was investigating whether eggs and seeds could survive travel across seawater to spread species across oceans. Hooker increasingly doubted the traditional view that species were fixed, but their young friend Thomas Henry Huxley was firmly against the transmutation of species. Lyell was intrigued by Darwin's speculations without realising their extent.