Last universal common ancestor

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Last_universal_common_ancestor

Phylogenetic tree linking all major groups of living organisms, namely the bacteria, archaea, and eukaryota, with the last universal common ancestor (LUCA) shown at the root

The last universal common ancestor (LUCA) is the hypothesized latest common ancestral cell population from which all subsequent life forms descend, including Bacteria, Archaea, and Eukarya. The cell had a lipid bilayer; it possessed the genetic code and ribosomes which translated from DNA or RNA to proteins. Although the timing of the LUCA cannot be definitively constrained, most studies suggest that the LUCA existed by 3.5 billion years ago, and possibly as early as 4.3 billion years ago or earlier. The nature of this point or stage of divergence remains a topic of research.

All earlier forms of life preceding this divergence and all extant organisms are generally thought to share common ancestry. On the basis of a formal statistical test, this theory of a universal common ancestry (UCA) is supported in preference to competing multiple-ancestry hypotheses. The first universal common ancestor (FUCA) is a hypothetical non-cellular ancestor to LUCA and other now-extinct sister lineages.

Whether the genesis of viruses falls before or after the LUCA–as well as the diversity of extant viruses and their hosts–remains a subject of investigation.

While no fossil evidence of the LUCA exists, the detailed biochemical similarity of all current life (divided into the three domains) makes its existence widely accepted by biochemists. Its characteristics can be inferred from shared features of modern genomes. These genes describe a complex life form with many co-adapted features, including transcription and translation mechanisms to convert information from DNA to mRNA to proteins.

Historical background

Further information: Tree of life (biology)

A tree of life, like this one from Charles Darwin's notebooks c. July 1837, implies a single common ancestor at its root (labelled "1").

A phylogenetic tree directly portrays the idea of evolution by descent from a single ancestor. An early tree of life was sketched by Jean-Baptiste Lamarck in his Philosophie zoologique in 1809. Charles Darwin more famously proposed the theory of universal common descent through an evolutionary process in his book On the Origin of Species in 1859: "Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed." The last sentence of the book begins with a restatement of the hypothesis:

There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one ...

By 1871, in another letter to Hooker, Darwin speculated on the natural origin of life itself, writing that life might have begun in a "warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present", an early expression of abiogenesis.

The term "last universal common ancestor" or "LUCA" was first used in the 1990s for such a primordial organism.

Inferring LUCA's features

Biochemical mechanisms

While the anatomy of LUCA cannot be reconstructed with certainty, its biochemical mechanisms can be deduced and described in some detail, based on properties shared by currently living organisms as well as genetic analysis.

LUCA certainly had genes and a genetic code. Its genetic material was most likely DNA, so that it lived after the RNA world. The DNA was kept double-stranded by an enzyme, DNA polymerase, which recognises the structure and directionality of DNA. The integrity of the DNA was maintained by a group of repair enzymes including DNA topoisomerase. If the genetic code was based on dual-stranded DNA, it was expressed by copying the information to single-stranded RNA. The RNA was produced by a DNA-dependent RNA polymerase using nucleotides similar to those of DNA. It had multiple DNA-binding proteins, such as histone-fold proteins. The genetic code was expressed into proteins. These were assembled from 20 free amino acids by translation of a messenger RNA via a mechanism of ribosomes, transfer RNAs, and a group of related proteins.

Although LUCA was likely not capable of sexual interaction, gene functions were present that promoted the transfer of DNA between individuals of the population to facilitate genetic recombination. Homologous gene products that promote genetic recombination are present in bacteria, archaea and eukaryota, such as the RecA protein in bacteria, the RadA protein in archaea, and the Rad51 and Dmc1 proteins in eukaryota.

LUCA's functionality, and evidence for the early evolution of membrane-dependent biological systems, together suggest that LUCA was a cell with membranes. It contained a water-based cytoplasm enclosed by a lipid bilayer membrane; it reproduced by cell division. It tended to exclude sodium and concentrate potassium by means of specific ion transporters (or ion pumps). The cell multiplied by duplicating all its contents followed by cellular division. The cell used chemiosmosis to produce energy. It also reduced CO₂ and oxidized H₂ (methanogenesis or acetogenesis) via acetyl-thioesters.

By phylogenetic bracketing, analysis of its offspring groups, LUCA appears to have been a small, single-celled organism. It likely had a ring-shaped coil of DNA floating freely within the cell. Morphologically, it would likely not have stood out within a mixed population of small modern-day bacteria. The originator of the three-domain system, Carl Woese, stated that in its genetic machinery, the LUCA would have been a "simpler, more rudimentary entity than the individual ancestors that spawned the three [domains] (and their descendants)".

Because bacteria and archaea differ in their structure of phospholipids and cell wall, ion pumping, most proteins involved in DNA replication, and glycolysis, it is inferred that LUCA had a permeable membrane without an ion pump. The emergence of Na⁺/H⁺ antiporters likely led to the later evolution of impermeable membranes in eukaryotes, archaea, and bacteria. This would accord with LUCA's having made use of the natural geochemical proton gradient in its environment across a leaky membrane to provide it with energy. Cell walls, too, would have evolved later. Although LUCA likely had DNA, it is unknown if it could replicate DNA: as Weiss et al write, it "might just have been a chemically stable repository for RNA-based replication". It is likely that LUCA's permeable membrane was composed of archaeal lipids (isoprenoids) and bacterial lipids (fatty acids). Isoprenoids would have helped to stabilize LUCA's membrane in the surrounding extreme habitat.

LUCA's genome was likely similar in size to that of modern prokaryotes, encoding around 2,600 proteins, based on statistical inference using the probabilistic gene- and species-tree reconciliation algorithm ALE. It may have been an acetogen, respiring anaerobically, and may have had an early CAS-based anti-viral immune system. The inferred metabolic features are consistent with the early Earth hydrothermal systems with high concentrations of CO₂ and H₂.

An anaerobic thermophile

Further information: Phylogenetic bracketing

 

A direct way to infer LUCA's genome would be to find genes common to all surviving descendants, but little can be learnt by this approach, as there are only about 30 such genes. They are mostly for ribosome proteins, proving that LUCA had the genetic code. Many other LUCA genes have been lost in later lineages over 4 billion years of evolution.

Three ways to infer genes present in LUCA: universal presence, presence in both the Bacterial and Archaean domains, and presence in two phyla in both domains. The first yields as stated only about 30 genes; the second, some 11,000 with lateral gene transfer (LGT) very likely; the third, 355 genes probably in LUCA, since they were found in at least two phyla in both domains, making LGT an unlikely explanation.

An alternative to the search for "universal" traits is to use genome analysis to identify phylogenetically ancient genes. This gives a picture of a LUCA that could live in a geochemically harsh environment and is like modern prokaryotes. Analysis of biochemical pathways implies the same sort of chemistry as does phylogenetic analysis.

LUCA systems and environment, including the Wood–Ljungdahl or reductive acetyl–CoA pathway to fix carbon, and most likely DNA complete with the genetic code and enzymes to replicate it, transcribe it to RNA, and translate it to proteins.

In 2016, Madeline C. Weiss and colleagues genetically analyzed 6.1 million protein-coding genes and 286,514 protein clusters from sequenced prokaryotic genomes representing many phylogenetic trees, and identified 355 protein clusters that were probably common to the LUCA. The results of their analysis are highly specific, though debated. They depict LUCA as "anaerobic, CO₂-fixing, H₂-dependent with a Wood–Ljungdahl pathway (the reductive acetyl-coenzyme A pathway), N₂-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms." The cofactors indicate "dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosylmethionine-dependent methylations." They show that methanogens and clostridia were basal, near the root of the phylogenetic tree, in the 355 protein lineages examined, and that the LUCA may therefore have inhabited an anaerobic hydrothermal vent setting in a geochemically active environment rich in H₂, CO₂, and iron, where ocean water interacted with hot magma beneath the ocean floor. It is inferred that LUCA grew from H₂ and CO₂ via the reverse incomplete Krebs cycle. Other metabolic pathways inferred in LUCA are the pentose phosphate pathway, glycolysis, and gluconeogenesis. Even if phylogenetic evidence may point to a hydrothermal vent environment for a thermophilic LUCA, this does not constitute evidence that the origin of life took place at a hydrothermal vent since mass extinctions may have removed previously existing branches of life.

The LUCA used the Wood–Ljungdahl or reductive acetyl–CoA pathway to fix carbon, if it was an autotroph, or to respire anaerobically, if it was a heterotroph.

Weiss and colleagues write that "Experiments ... demonstrate that ... acetyl-CoA pathway [chemicals used in anaerobic respiration] formate, methanol, acetyl moieties, and even pyruvate arise spontaneously ... from CO₂, native metals, and water", a combination present in hydrothermal vents.

An experiment shows that Zn²⁺, Cr³⁺, and Fe can promote 6 of the 11 reactions of an ancient anabolic pathway called the reverse Krebs cycle in acidic conditions which implies that LUCA might have inhabited either hydrothermal vents or acidic metal-rich hydrothermal fields.

Undersampled protein families

Some other researchers have challenged Weiss et al.'s 2016 conclusions. Sarah Berkemer and Shawn McGlynn argue that Weiss et al. undersampled the families of proteins, so that the phylogenetic trees were not complete and failed to describe the evolution of proteins correctly. There are two risks in attempting to attribute LUCA's environment from near-universal gene distribution (as in Weiss et al. 2016). On the one hand, it risks misattributing convergence or horizontal gene transfer events to vertical descent; on the other hand, it risks misattributing potential LUCA gene families as horizontal gene transfer events. A phylogenomic and geochemical analysis of a set of proteins that probably traced to the LUCA show that it had K⁺-dependent GTPases and the ionic composition and concentration of its intracellular fluid was seemingly high K⁺/Na⁺ ratio, NH⁺
₄, Fe²⁺, CO²⁺, Ni²⁺, Mg²⁺, Mn²⁺, Zn²⁺, pyrophosphate, and PO³⁻
₄ which would imply a terrestrial hot spring habitat. It possibly had a phosphate-based metabolism. Further, these proteins were unrelated to autotrophy (the ability of an organism to create its own organic matter), suggesting that the LUCA had a Heterotrophic lifestyle (consuming organic matter) and that its growth was dependent on organic matter produced by the physical environment.

The presence of the energy-handling enzymes CODH/acetyl-coenzyme A synthase in LUCA could be compatible with being an autotroph and with life as a mixotroph or heterotroph. Weiss et al. in 2018 replied that no enzyme defines a trophic lifestyle, and that heterotrophs evolved from autotrophs.

A 2024 study directly estimated the order in which amino acids were added into the genetic code from early protein domain sequences. A total of 969 protein domains were classified as present in LUCA, including 101 domain sequences that dated back to the even-older pre-LUCA communities. 88% of the protein domains annotated as LUCA or pre-LUCA were confirmed by Moody et al. 2024, by being associated with proteins that are more than 50% likely to be present in LUCA. It found that amino acids that bind metals, and those that contain sulphur, came early in the genetic code. The study suggests that sulphur metabolism and catalysis involving metals were important elements of life at the time of LUCA.

Possibly a mesophile

Several lines of evidence suggest that LUCA was non-thermophilic. The content of G + C nucleotide pairs (compared to the occurrence of A + T pairs) can indicate an organism's thermal optimum as they are more thermally stable due to an additional hydrogen bond. As a result, they occur more frequently in the rRNA of thermophiles; however, this is not seen in LUCA's reconstructed rRNA.

The identification of thermophilic genes in the LUCA has been challenged, as they may instead represent genes that evolved later in archaea or bacteria, then migrated between these via horizontal gene transfer, as in Woese's 1998 hypothesis. For instance, the thermophile-specific topoisomerase, reverse gyrase, was initially attributed to LUCA before an exhaustive phylogenetic study revealed a more recent origin of this enzyme followed by extensive horizontal gene transfer. LUCA could have been a mesophile that fixed CO₂ and relied on H₂, and lived close to hydrothermal vents.

Further evidence that LUCA was mesophilic comes from the amino acid composition of its proteins. The abundance of I, V, Y, W, R, E, and L amino acids (denoted IVYWREL) in an organism's proteins is correlated with its optimal growth temperature. According to phylogenetic analysis, the IVYWREL content of LUCA's proteins suggests its ideal temperature was below 50°C.

Evidence that bacteria and archaea both independently underwent phases of increased and subsequently decreased thermo-tolerance suggests a dramatic post-LUCA climate shift that affected both populations, and would explain the seeming genetic pervasiveness of thermo-tolerant genetics.

Age

Further information: Abiogenesis

Studies from 2000 to 2018 have suggested an increasingly ancient time for the LUCA. In 2000, estimates of the LUCA's age ranged from 3.8 to 3.5 bya (billion years ago) in the Paleoarchean, a few hundred million years after the earliest fossil evidence of life, for which candidates range in age from 4.28 to 3.48 bya. This placed the origin of the first forms of life shortly after the Late Heavy Bombardment which was thought to have repeatedly sterilized Earth's surface. However, a 2018 study by Holly Betts and colleagues applied a molecular clock model to the genomic and fossil record (102 species, 29 common protein-coding genes, mostly ribosomal), concluding that LUCA preceded the Late Heavy Bombardment (making the LUCA over 3.9 bya). A 2022 study suggested an age of around 4.2–3.6 bya for the LUCA. A 2024 study suggested that the LUCA lived around 4.2 bya (with a confidence interval of 4.33–4.09 bya). This 2024 dating implies that the time gap between the origin of life and LUCA is only about 100-200 million years, as the first habitable environments likely formed around 4.3 or 4.4 bya.

Root of the tree of life

For branching of bacteria phyla, see Bacterial phyla.

2005 tree of life showing horizontal gene transfers between branches including (coloured lines) the symbiogenesis of plastids and mitochondria. "Horizontal gene transfer and how it has impacted the evolution of life is presented through a web connecting bifurcating branches that complicate, yet do not erase, the tree of life".

In 1990, a novel concept of the tree of life was presented, dividing the living world into three stems, classified as the domains Bacteria, Archaea, Eukarya. It is the first tree founded exclusively on molecular phylogenetics, and which includes the evolution of microorganisms. It has been called a "universal phylogenetic tree in rooted form". This tree and its rooting became the subject of debate.

In the meantime, numerous modifications of this tree, mainly concerning the role and importance of horizontal gene transfer for its rooting and early ramifications have been suggested. Since heredity occurs both vertically and horizontally, the tree of life may have been more weblike or netlike in its early phase and more treelike when it grew three-stemmed. Presumably horizontal gene transfer has decreased with growing cell stability.

A modified version of the tree, based on several molecular studies, has its root between a monophyletic domain Bacteria and a clade formed by Archaea and Eukaryota. A small minority of studies place the root in the domain bacteria, in the phylum Bacillota, or state that the phylum Chloroflexota (formerly Chloroflexi) is basal to a clade with Archaea and Eukaryotes and the rest of bacteria (as proposed by Thomas Cavalier-Smith). Metagenomic analyses recover a two-domain system with the domains Archaea and Bacteria; in this view of the tree of life, Eukaryotes are derived from Archaea. With the later gene pool of LUCA's descendants, sharing a common framework of the AT/GC rule and the standard twenty amino acids, horizontal gene transfer would have become feasible and could have been common.

The nature of LUCA remains disputed. In 1994, on the basis of primordial metabolism (as discussed by Wächtershäuser), Otto Kandler proposed a successive divergence of the three domains of life from a multiphenotypical population of pre-cells, reached by gradual evolutionary improvements (cellularization). The phenotypically diverse pre-cells of this population were metabolising, self-reproducing entities exhibiting frequent mutual exchange of genetic information. Thus, in this scenario there was no "first cell". It may explain the unity and, at the same time, the partition into three lines (the three domains) of life. Kandler's pre-cell theory is supported by Wächtershäuser. In 1998, Carl Woese, based on the RNA world concept, proposed that no individual organism could be considered a LUCA, and that the genetic heritage of all modern organisms derived through horizontal gene transfer among an ancient community of organisms. Other authors concur that there was a "complex collective genome" at the time of the LUCA, and that horizontal gene transfer was important in the evolution of later groups; Nicolas Glansdorff states that LUCA "was in a metabolically and morphologically heterogeneous community, constantly shuffling around genetic material" and "remained an evolutionary entity, though loosely defined and constantly changing, as long as this promiscuity lasted."

The theory of a universal common ancestry of life is widely accepted. In 2010, based on "the vast array of molecular sequences now available from all domains of life", D. L. Theobald published a "formal test" of universal common ancestry (UCA). This deals with the common descent of all extant terrestrial organisms, each being a genealogical descendant of a single species from the distant past. His formal test favoured the existence of a universal common ancestry over a wide class of alternative hypotheses that included horizontal gene transfer. Basic biochemical principles imply that all organisms do have a common ancestry.

A proposed non-cellular ancestor to LUCA is the first universal common ancestor (FUCA). FUCA would therefore be the ancestor to every modern cell as well as to ancient, now-extinct cellular lineages not descending from LUCA. FUCA is assumed to have had descendants other than LUCA, none of which have modern descendants. Some genes of these ancient now-extinct cell lineages are thought to have been horizontally transferred into the genome of early descendants of LUCA.

LUCA and viruses

The origin of viruses remains disputed. Since viruses need host cells for their replication, it is likely that they emerged after the formation of cells. Viruses may even have multiple origins and different types of viruses may have evolved independently over the history of life. There are different hypotheses for the origins of viruses, for instance an early viral origin from the RNA world or a later viral origin from selfish DNA.

Based on how viruses are currently distributed across the bacteria and archaea, the LUCA is suspected of having been prey to multiple viruses, ancestral to those that now have those two domains as their hosts. Furthermore, extensive virus evolution seems to have preceded the LUCA, since the jelly-roll structure of capsid proteins is shared by RNA and DNA viruses across all three domains of life. LUCA's viruses were probably mainly dsDNA viruses in the groups called Duplodnaviria and Varidnaviria. Two other single-stranded DNA virus groups within the Monodnaviria, the Microviridae and the Tubulavirales, likely infected the last bacterial common ancestor. The last archaeal common ancestor was probably host to spindle-shaped viruses. All of these could well have affected the LUCA, in which case each must since have been lost in the host domain where it is no longer extant. By contrast, RNA viruses do not appear to have been important parasites of LUCA, even though straightforward thinking might have envisaged viruses as beginning with RNA viruses directly derived from an RNA world. Instead, by the time the LUCA lived, RNA viruses had probably already been out-competed by DNA viruses.

LUCA might have been the ancestor of some viruses, with one of its descendants being the archaic virocell ancestor, the ancestor to large-to-medium-sized DNA viruses. The distribution pattern of DNA viruses in the tree of life also supports the hypothesis that DNA viruses originated from RNA-based LUCA. Viruses could equally have evolved before LUCA but after the first universal common ancestor (FUCA), according to the reduction hypothesis, where giant viruses evolved from primordial cells that became parasitic.

Selective breeding

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Selective_breeding 

Mutation and selection

A Belgian Blue cow. The defect in the breed's myostatin gene is maintained through linebreeding and is responsible for its accelerated lean muscle growth.

This Chihuahua mix and Great Dane shows the wide range of dog breed sizes created using selective breeding.

Selective breeding transformed teosinte's few fruitcases (left) into modern maize's rows of exposed kernels (right).

Selective breeding (also called artificial selection) is the process by which humans use animal breeding and plant breeding to selectively develop particular phenotypic traits (characteristics) by choosing which typically animal or plant males and females will sexually reproduce and have offspring together. Domesticated animals are known as breeds, normally bred by a professional breeder, while domesticated plants are known as varieties, cultigens, cultivars, or breeds. Two purebred animals of different breeds produce a crossbreed, and crossbred plants are called hybrids. Flowers, vegetables and fruit-trees may be bred by amateurs and commercial or non-commercial professionals: major crops are usually the provenance of the professionals.

In animal breeding artificial selection is often combined with techniques such as inbreeding, linebreeding, and outcrossing. In plant breeding, similar methods are used. Charles Darwin discussed how selective breeding had been successful in producing change over time in his 1859 book, On the Origin of Species. Its first chapter discusses selective breeding and domestication of such animals as pigeons, cats, cattle, and dogs. Darwin used artificial selection as an analogy to propose and explain the theory of natural selection but distinguished the latter from the former as a separate process that is non-directed.

The deliberate exploitation of selective breeding to produce desired results has become very common in agriculture and experimental biology.

Selective breeding can be unintentional, for example, resulting from the process of human cultivation; and it may also produce unintended – desirable or undesirable – results. For example, in some grains, an increase in seed size may have resulted from certain ploughing practices rather than from the intentional selection of larger seeds. Most likely, there has been an interdependence between natural and artificial factors that have resulted in plant domestication.

History

Selective breeding of both plants and animals has been practiced since prehistory; key species such as wheat, rice, and dogs have been significantly different from their wild ancestors for millennia, and maize, which required especially large changes from teosinte, its wild form, was selectively bred in Mesoamerica. Selective breeding was practiced by the Romans. Treatises as much as 2,000 years old give advice on selecting animals for different purposes, and these ancient works cite still older authorities, such as Mago the Carthaginian. The notion of selective breeding was later expressed by the polymath Abu Rayhan Biruni in the 11th century. He noted the idea in his book titled India, which included various examples.

The agriculturist selects his corn, letting grow as much as he requires, and tearing out the remainder. The forester leaves those branches which he perceives to be excellent, whilst he cuts away all others. The bees kill those of their kind who only eat, but do not work in their beehive.

— Abu Rayhan Biruni, India

Selective breeding was established as a scientific practice by Robert Bakewell during the British Agricultural Revolution in the 18th century. Arguably, his most important breeding program was with sheep. Using native stock, he was able to quickly select for large, yet fine-boned sheep, with long, lustrous wool. The Lincoln Longwool was improved by Bakewell, and in turn the Lincoln was used to develop the subsequent breed, named the New (or Dishley) Leicester. It was hornless and had a square, meaty body with straight top lines.

These sheep were exported widely, including to Australia and North America, and have contributed to numerous modern breeds, despite the fact that they fell quickly out of favor as market preferences in meat and textiles changed. Bloodlines of these original New Leicesters survive today as the English Leicester (or Leicester Longwool), which is primarily kept for wool production.

Bakewell was also the first to breed cattle to be used primarily for beef. Previously, cattle were first and foremost kept for pulling ploughs as oxen, but he crossed long-horned heifers and a Westmoreland bull to eventually create the Dishley Longhorn. As more and more farmers followed his lead, farm animals increased dramatically in size and quality. In 1700, the average weight of a bull sold for slaughter was 370 pounds (168 kg). By 1786, that weight had more than doubled to 840 pounds (381 kg). However, after his death, the Dishley Longhorn was replaced with short-horn versions.

He also bred the Improved Black Cart horse, which later became the Shire horse.

Charles Darwin coined the term 'selective breeding'; he was interested in the process as an illustration of his proposed wider process of natural selection. Darwin noted that many domesticated animals and plants had special properties that were developed by intentional animal and plant breeding from individuals that showed desirable characteristics, and discouraging the breeding of individuals with less desirable characteristics.

Darwin used the term "artificial selection" twice in the 1859 first edition of his work On the Origin of Species, in Chapter IV: Natural Selection, and in Chapter VI: Difficulties on Theory:

Slow though the process of selection may be, if feeble man can do much by his powers of artificial selection, I can see no limit to the amount of change, to the beauty and infinite complexity of the co-adaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature's power of selection.

— Charles Darwin, On the Origin of Species

We are profoundly ignorant of the causes producing slight and unimportant variations; and we are immediately made conscious of this by reflecting on the differences in the breeds of our domesticated animals in different countries,—more especially in the less civilized countries where there has been but little artificial selection.

— Charles Darwin, On the Origin of Species

Animal breeding

Main article: Animal breeding

Animals with homogeneous appearance, behavior, and other characteristics are known as particular breeds or pure breeds, and they are bred through culling animals with particular traits and selecting for further breeding those with other traits. Purebred animals belong to a single, recognizable breed, and purebreds with recorded lineage are called pedigreed. Crossbreeds are a mix of two purebreds, whereas mixed breeds are a mix of several breeds, often unknown. Animal breeding begins with breeding stock, a group of animals used for the purpose of planned breeding. When individuals are looking to breed animals, they look for certain valuable traits in purebred stock for a certain purpose, or may intend to use some type of crossbreeding to produce a new type of stock with different and presumably superior abilities in a given area of endeavor. For example, to breed chickens, a breeder typically intends to receive eggs, meat, and new, young birds for further reproduction. Thus, the breeder has to study different breeds and types of chickens and analyze what can be expected from a certain set of characteristics before he or she starts breeding them. Therefore, when purchasing initial breeding stock, the breeder seeks a group of birds that will most closely fit the purpose intended.

Purebred breeding aims to establish and maintain stable traits, that animals will pass to the next generation. By "breeding the best to the best," employing a certain degree of inbreeding, considerable culling, and selection for "superior" qualities, one could develop a bloodline superior in certain respects to the original base stock. Such animals can be recorded with a breed registry, the organization that maintains pedigrees and/or stud books. However, single-trait breeding, breeding for only one trait over all others, can be problematic. In one case mentioned by the animal behaviorist Temple Grandin, roosters bred for fast growth or heavy muscles did not know how to perform typical rooster courtship dances, which alienated the roosters from hens and led the roosters to kill the hens after mating with them. A Soviet attempt to breed lab rats with higher intelligence led to cases of neurosis severe enough to make the animals incapable of any problem solving unless drugs like phenazepam were used.

The observable phenomenon of hybrid vigor stands in contrast to the notion of breed purity. However, on the other hand, indiscriminate breeding of crossbred or hybrid animals may also result in degradation of quality. Studies in evolutionary physiology, behavioral genetics, and other areas of organismal biology have also made use of deliberate selective breeding, though longer generation times and greater difficulty in breeding can make these projects challenging in such vertebrates as house mice.

Plant breeding

Main article: Plant breeding

Researchers at the USDA have selectively bred carrots with a variety of colors.

The process of plant breeding has been used for thousands of years, and began with the domestication of wild plants into uniform and predictable agricultural cultigens. These high-yielding varieties have been particularly important in agriculture. As crops improved, humans were able to move from hunter-gatherer style living to a mix of hunter-gatherer and agriculture practices. Although these higher yielding plants were derived from an extremely primitive version of plant breeding, this form of agriculture was an investment that the people who grew them were planting then could have a more varied diet. This meant that they did not completely stop their hunting and gathering immediately but instead over time transitioned and ultimately favored agriculture. Originally this was due to humans not wanting to risk using all their time and resources for their crops just to fail. Which was promptly called play farming due to the idea of "farmers" experimenting with agriculture. In addition, the ability for humans to stay within one place for food and create permanent settlements made the process move along faster.^[20] During this transitional period, crops began to acclimate and evolve with humans encouraging humans to invest further into crops. Over time this reliance on plant breeding has created problems, as highlighted by the book Botany of Desire where Michael Pollan shows the connection between basic human desires through four different plants: apples for sweetness, tulips for beauty, cannabis for intoxication, and potatoes for control. In a form of coevolution humans have influenced these plants as much as the plants have influenced the people that consume them

Selective plant breeding is also used in research to produce transgenic animals that breed "true" (i.e., are homozygous) for artificially inserted or deleted genes.

Selective breeding in aquaculture

Selective breeding in aquaculture holds high potential for the genetic improvement of fish and shellfish for the process of production. Unlike terrestrial livestock, the potential benefits of selective breeding in aquaculture were not realized until recently. This is because high mortality led to the selection of only a few broodstock, causing inbreeding depression, which then forced the use of wild broodstock. This was evident in selective breeding programs for growth rate, which resulted in slow growth and high mortality.

Control of the reproduction cycle was one of the main reasons as it is a requisite for selective breeding programs. Artificial reproduction was not achieved because of the difficulties in hatching or feeding some farmed species such as eel and yellowtail farming. A suspected reason associated with the late realization of success in selective breeding programs in aquaculture was the education of the concerned people – researchers, advisory personnel and fish farmers. The education of fish biologists paid less attention to quantitative genetics and breeding plans.

Another was the failure of documentation of the genetic gains in successive generations. This in turn led to failure in quantifying economic benefits that successful selective breeding programs produce. Documentation of the genetic changes was considered important as they help in fine tuning further selection schemes.

Quality traits in aquaculture

Aquaculture species are reared for particular traits such as growth rate, survival rate, meat quality, resistance to diseases, age at sexual maturation, fecundity, shell traits like shell size, shell color, etc.

• Growth rate – growth rate is normally measured as either body weight or body length. This trait is of great economic importance for all aquaculture species as faster growth rate speeds up the turnover of production. Improved growth rates show that farmed animals utilize their feed more efficiently through a positive correlated response.
• Survival rate – survival rate may take into account the degrees of resistance to diseases. This may also see the stress response as fish under stress are highly vulnerable to diseases. The stress fish experience could be of biological, chemical or environmental influence.
• Meat quality – the quality of fish is of great economic importance in the market. Fish quality usually takes into account size, meatiness, and percentage of fat, color of flesh, taste, shape of the body, ideal oil and omega-3 content.
• Age at sexual maturation – The age of maturity in aquaculture species is another very important attribute for farmers as during early maturation the species divert all their energy to gonad production affecting growth and meat production and are more susceptible to health problems (Gjerde 1986).
• Fecundity – As the fecundity in fish and shellfish is usually high it is not considered as a major trait for improvement. However, selective breeding practices may consider the size of the egg and correlate it with survival and early growth rate.

Finfish response to selection

Salmonids

Gjedrem (1979) showed that selection of Atlantic salmon (Salmo salar) led to an increase in body weight by 30% per generation. A comparative study on the performance of select Atlantic salmon with wild fish was conducted by AKVAFORSK Genetics Centre in Norway. The traits, for which the selection was done included growth rate, feed consumption, protein retention, energy retention, and feed conversion efficiency. Selected fish had a twice better growth rate, a 40% higher feed intake, and an increased protein and energy retention. This led to an overall 20% better Fed Conversion Efficiency as compared to the wild stock. Atlantic salmon have also been selected for resistance to bacterial and viral diseases. Selection was done to check resistance to Infectious Pancreatic Necrosis Virus (IPNV). The results showed 66.6% mortality for low-resistant species whereas the high-resistant species showed 29.3% mortality compared to wild species.

Rainbow trout (S. gairdneri) was reported to show large improvements in growth rate after 7–10 generations of selection. Kincaid et al. (1977) showed that growth gains by 30% could be achieved by selectively breeding rainbow trout for three generations. A 7% increase in growth was recorded per generation for rainbow trout by Kause et al. (2005).

In Japan, high resistance to IPNV in rainbow trout has been achieved by selectively breeding the stock. Resistant strains were found to have an average mortality of 4.3% whereas 96.1% mortality was observed in a highly sensitive strain.

Coho salmon (Oncorhynchus kisutch) increase in weight was found to be more than 60% after four generations of selective breeding. In Chile, Neira et al. (2006) conducted experiments on early spawning dates in coho salmon. After selectively breeding the fish for four generations, spawning dates were 13–15 days earlier.

Cyprinids

Selective breeding programs for the Common carp (Cyprinus carpio) include improvement in growth, shape and resistance to disease. Experiments carried out in the USSR used crossings of broodstocks to increase genetic diversity and then selected the species for traits like growth rate, exterior traits and viability, and/or adaptation to environmental conditions like variations in temperature. Kirpichnikov et al. (1974) and Babouchkine (1987) selected carp for fast growth and tolerance to cold, the Ropsha carp. The results showed a 30–40% to 77.4% improvement of cold tolerance but did not provide any data for growth rate. An increase in growth rate was observed in the second generation in Vietnam. Moav and Wohlfarth (1976) showed positive results when selecting for slower growth for three generations compared to selecting for faster growth. Schaperclaus (1962) showed resistance to the dropsy disease wherein selected lines suffered low mortality (11.5%) compared to unselected (57%).

Channel Catfish

Growth was seen to increase by 12–20% in selectively bred Iictalurus punctatus. More recently, the response of the Channel Catfish to selection for improved growth rate was found to be approximately 80%, that is, an average of 13% per generation.

Shellfish response to selection

Oysters

Selection for live weight of Pacific oysters showed improvements ranging from 0.4% to 25.6% compared to the wild stock. Sydney-rock oysters (Saccostrea commercialis) showed a 4% increase after one generation and a 15% increase after two generations. Chilean oysters (Ostrea chilensis), selected for improvement in live weight and shell length showed a 10–13% gain in one generation. Bonamia ostrea is a protistan parasite that causes catastrophic losses (nearly 98%) in European flat oyster Ostrea edulis L. This protistan parasite is endemic to three oyster-regions in Europe. Selective breeding programs show that O. edulis susceptibility to the infection differs across oyster strains in Europe. A study carried out by Culloty et al. showed that 'Rossmore' oysters in Cork harbour, Ireland had better resistance compared to other Irish strains. A selective breeding program at Cork harbour uses broodstock from 3– to 4-year-old survivors and is further controlled until a viable percentage reaches market size.

Over the years 'Rossmore' oysters have shown to develop lower prevalence of B. ostreae infection and percentage mortality. Ragone Calvo et al. (2003) selectively bred the eastern oyster, Crassostrea virginica, for resistance against co-occurring parasites Haplosporidium nelson (MSX) and Perkinsus marinus (Dermo). They achieved dual resistance to the disease in four generations of selective breeding. The oysters showed higher growth and survival rates and low susceptibility to the infections. At the end of the experiment, artificially selected C. virginica showed a 34–48% higher survival rate.

Penaeid shrimps

Selection for growth in Penaeid shrimps yielded successful results. A selective breeding program for Litopenaeus stylirostris saw an 18% increase in growth after the fourth generation and 21% growth after the fifth generation. Marsupenaeus japonicas showed a 10.7% increase in growth after the first generation. Argue et al. (2002) conducted a selective breeding program on the Pacific White Shrimp, Litopenaeus vannamei at The Oceanic Institute, Waimanalo, USA from 1995 to 1998. They reported significant responses to selection compared to the unselected control shrimps. After one generation, a 21% increase was observed in growth and 18.4% increase in survival to TSV. The Taura Syndrome Virus (TSV) causes mortalities of 70% or more in shrimps. C.I. Oceanos S.A. in Colombia selected the survivors of the disease from infected ponds and used them as parents for the next generation. They achieved satisfying results in two or three generations wherein survival rates approached levels before the outbreak of the disease. The resulting heavy losses (up to 90%) caused by Infectious hypodermal and haematopoietic necrosis virus (IHHNV) caused a number of shrimp farming industries started to selectively breed shrimps resistant to this disease. Successful outcomes led to development of Super Shrimp, a selected line of L. stylirostris that is resistant to IHHNV infection. Tang et al. (2000) confirmed this by showing no mortalities in IHHNV- challenged Super Shrimp post larvae and juveniles.

Aquatic species versus terrestrial livestock

Selective breeding programs for aquatic species provide better outcomes compared to terrestrial livestock. This higher response to selection of aquatic farmed species can be attributed to the following:

• High fecundity in both sexes fish and shellfish enabling higher selection intensity.
• Large phenotypic and genetic variation in the selected traits.

Selective breeding in aquaculture provide remarkable economic benefits to the industry, the primary one being that it reduces production costs due to faster turnover rates. When selective breeding is carried out, some characteristics are lost for others that may suit a specific environment or situation. This is because of faster growth rates, decreased maintenance rates, increased energy and protein retention, and better feed efficiency. Applying genetic improvement programs to aquaculture species will increase their productivity. Thus allowing them to meet the increasing demands of growing populations. Conversely, selective breeding within aquaculture can create problems within the biodiversity of both stock and wild fish, which can hurt the industry down the road. Although there is great potential to improve aquaculture due to the current lack of domestication, it is essential that the genetic diversity of the fish are preserved through proper genetic management, as we domesticate these species. It is not uncommon for fish to escape the nets or pens that they are kept in, especially in mass. If these fish are farmed in areas they are not native to they may be able to establish themselves and outcompete native populations of fish, and cause ecological harm as an invasive species. Furthermore, if they are in areas where the fish being farmed are native too their genetics are selectively bred rather than being wild. These farmed fish could breed with the natives which could be problematic In the sense that they would have been bred for consumption rather than by chance. Resulting in an overall decrease in genetic diversity and rendering local fish populations less fit for survival. If proper management is not taking place then the economic benefits and the diversity of the fish species will falter.

Advantages and disadvantages

Selective breeding is a direct way to determine if a specific trait can evolve in response to selection. A single-generation method of breeding is not as accurate or direct. The process is also more practical and easier to understand than sibling analysis. Selective breeding is better for traits such as physiology and behavior that are hard to measure because it requires fewer individuals to test than single-generation testing.

However, there are disadvantages to this process. This is because a single experiment done in selective breeding cannot be used to assess an entire group of genetic variances, individual experiments must be done for every individual trait. Also, due to the necessity of selective breeding experiments to require maintaining the organisms tested in a lab or greenhouse, it is impractical to use this breeding method on many organisms. Controlled mating instances are difficult to carry out in this case and this is a necessary component of selective breeding.

Additionally, selective breeding can lead to a variety of issues including reduction of genetic diversity or physical problems. The process of selective breeding can create physical issues for plants or animals such as dogs selectively bred for extremely small sizes dislocating their kneecaps at a much more frequent rate then other dogs. An example in the plant world is the Lenape potatoes were selectively bred for their disease or pest resistance which was attributed to their high levels of toxic glycoalkaloid solanine which are usually present only in small amounts in potatoes fit for human consumption. When genetic diversity is lost it can also allow for populations to lack genetic alternatives to adapt to events. This becomes an issue of biodiversity, because attributes are so wide-spread they can result in mass epidemics. As seen in the Southern Corn leaf-blight epidemic of 1970 that wiped out 15% of the United States corn crop due to the wide use of a type of Texan corn strain that was artificially selected due to having sterile pollen to make farming easier. At the same time it was more vulnerable to Southern Corn leaf-blight.

Earth system science

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Earth_system_science 

An ecological analysis of CO
₂ in an ecosystem. As systems biology, systems ecology seeks a holistic view of the interactions and transactions within and between biological and ecological systems.

Earth system science (ESS) is the application of systems science to the Earth. In particular, it considers interactions and 'feedbacks', through material and energy fluxes, between the Earth's sub-systems' cycles, processes and "spheres"—atmosphere, hydrosphere, cryosphere, geosphere, pedosphere, lithosphere, biosphere, and even the magnetosphere—as well as the impact of human societies on these components. At its broadest scale, Earth system science brings together researchers across both the natural and social sciences, from fields including ecology, economics, geography, geology, glaciology, meteorology, oceanography, climatology, paleontology, sociology, and space science. Like the broader subject of systems science, Earth system science assumes a holistic view of the dynamic interaction between the Earth's spheres and their many constituent subsystems fluxes and processes, the resulting spatial organization and time evolution of these systems, and their variability, stability and instability. Subsets of Earth System science include systems geology and systems ecology, and many aspects of Earth System science are fundamental to the subjects of physical geography and climate science.

Definition

The Science Education Resource Center, Carleton College, offers the following description: "Earth System science embraces chemistry, physics, biology, mathematics and applied sciences in transcending disciplinary boundaries to treat the Earth as an integrated system. It seeks a deeper understanding of the physical, chemical, biological and human interactions that determine the past, current and future states of the Earth. Earth System science provides a physical basis for understanding the world in which we live and upon which humankind seeks to achieve sustainability".

Earth System science has articulated four overarching, definitive and critically important features of the Earth System, which include:

1. Variability: Many of the Earth System's natural 'modes' and variabilities across space and time are beyond human experience, because of the stability of the recent Holocene. Much Earth System science therefore relies on studies of the Earth's past behaviour and models to anticipate future behaviour in response to pressures.
2. Life: Biological processes play a much stronger role in the functioning and responses of the Earth System than previously thought. It appears to be integral to every part of the Earth System.
3. Connectivity: Processes are connected in ways and across depths and lateral distances that were previously unknown and inconceivable.
4. Non-linear: The behaviour of the Earth System is typified by strong non-linearities. This means that abrupt change can result when relatively small changes in a 'forcing function' push the System across a 'threshold'.

History

For millennia, humans have speculated how the physical and living elements on the surface of the Earth combine, with gods and goddesses frequently posited to embody specific elements. The notion that the Earth, itself, is alive was a regular theme of Greek philosophy and religion.

Early scientific interpretations of the Earth system began in the field of geology, initially in the Middle East and China, and largely focused on aspects such as the age of the Earth and the large-scale processes involved in mountain and ocean formation. As geology developed as a science, understanding of the interplay of different facets of the Earth system increased, leading to the inclusion of factors such as the Earth's interior, planetary geology, living systems and Earth-like worlds.

In many respects, the foundational concepts of Earth System science can be seen in the natural philosophy 19th century geographer Alexander von Humboldt. In the 20th century, Vladimir Vernadsky (1863–1945) saw the functioning of the biosphere as a geological force generating a dynamic disequilibrium, which in turn promoted the diversity of life.

In parallel, the field of systems science was developing across numerous other scientific fields, driven in part by the increasing availability and power of computers, and leading to the development of climate models that began to allow the detailed and interacting simulations of the Earth's weather and climate. Subsequent extension of these models has led to the development of "Earth system models" (ESMs) that include facets such as the cryosphere and the biosphere.

In 1983 a NASA committee called the Earth System Science Committee was formed. The earliest reports of NASA's ESSC, Earth System Science: Overview (1986), and the book-length Earth System Science: A Closer View (1988), constitute a major landmark in the formal development of Earth system science. Early works discussing Earth system science, like these NASA reports, generally emphasized the increasing human impacts on the Earth system as a primary driver for the need of greater integration among the life and geo-sciences, making the origins of Earth system science parallel to the beginnings of global change studies and programs.

Climate science

Climatology and climate change have been central to Earth System science since its inception, as evidenced by the prominent place given to climate change in the early NASA reports discussed above. The Earth's climate system is a prime example of an emergent property of the whole planetary system, that is, one which cannot be fully understood without regarding it as a single integrated entity. It is also a system where human impacts have been growing rapidly in recent decades, lending immense importance to the successful development and advancement of Earth System science research. As just one example of the centrality of climatology to the field, the mission statement of one of the earliest centers for Earth System science research, the Earth System Science Center at Pennsylvania State University, reads, "the Earth System Science Center (ESSC) maintains a mission to describe, model, and understand the Earth's climate system".

The five components of the climate system all interact. They are the atmosphere, the hydrosphere, the cryosphere, the lithosphere and the biosphere.

Earth's climate system is a complex system with five interacting components: the atmosphere (air), the hydrosphere (water), the cryosphere (ice and permafrost), the lithosphere (earth's upper rocky layer) and the biosphere (living things). Climate is the statistical characterization of the climate system. It represents the average weather, typically over a period of 30 years, and is determined by a combination of processes, such as ocean currents and wind patterns. Circulation in the atmosphere and oceans transports heat from the tropical regions to regions that receive less energy from the Sun. Solar radiation is the main driving force for this circulation. The water cycle also moves energy throughout the climate system. In addition, certain chemical elements are constantly moving between the components of the climate system. Two examples for these biochemical cycles are the carbon and nitrogen cycles.

The climate system can change due to internal variability and external forcings. These external forcings can be natural, such as variations in solar intensity and volcanic eruptions, or caused by humans. Accumulation of greenhouse gases in the atmosphere, mainly being emitted by people burning fossil fuels, is causing climate change. Human activity also releases cooling aerosols, but their net effect is far less than that of greenhouse gases. Changes can be amplified by feedback processes in the different climate system components.

Education

Earth System science can be studied at a postgraduate level at some universities. In general education, the American Geophysical Union, in cooperation with the Keck Geology Consortium and with support from five divisions within the National Science Foundation, convened a workshop in 1996, "to define common educational goals among all disciplines in the Earth sciences". In its report, participants noted that, "The fields that make up the Earth and space sciences are currently undergoing a major advancement that promotes understanding the Earth as a number of interrelated systems". Recognizing the rise of this systems approach, the workshop report recommended that an Earth System science curriculum be developed with support from the National Science Foundation.

In 2000, the Earth System Science Education Alliance (ESSEA) was begun, and currently includes the participation of 40+ institutions, with over 3,000 teachers having completed an ESSEA course as of fall 2009".

Related concepts

The concept of earth system law (still in its infancy as per 2021) is a sub-discipline of earth system governance, itself a subfield of earth system sciences analyzed from a social sciences perspective.