Phylogenetics

From Wikipedia, the free encyclopedia

In biology, phylogenetics /faɪlɵdʒɪˈnɛtɪks/ is the study of evolutionary relationships among groups of organisms (e.g. species, populations), which are discovered through molecular sequencing data and morphological data matrices. The term phylogenetics derives from the Greek terms phylé (φυλή) and phylon (φῦλον), denoting "tribe", "clan", "race"^[1] and the adjectival form, genetikós (γενετικός), of the word genesis (γένεσις) "origin", "source", "birth".

In fact, phylogenesis is the process, phylogeny is science on this process, and phylogenetics is phylogeny based on analysis of sequences of biological macromolecules (DNA, RNA and proteins, in the first).^[2] The result of phylogenetic studies is a hypothesis about the evolutionary history of taxonomic groups: their phylogeny.^[3]

Evolution is a process whereby populations are altered over time and may split into separate branches, hybridize together, or terminate by extinction. The evolutionary branching process may be depicted as a phylogenetic tree, and the place of each of the various organisms on the tree is based on a hypothesis about the sequence in which evolutionary branching events occurred. In historical linguistics, similar concepts are used with respect to relationships between languages; and in textual criticism with stemmatics.

Phylogenetic analyses have become essential to research on the evolutionary tree of life. For example, the RedToL aims at reconstructing the Red Algal Tree of Life. The National Science Foundation sponsors a project called the Assembling the Tree of Life (AToL) activity. The goal of this project is to determine evolutionary relationships across large groups of organisms throughout the history of life. The research on this project often involves large teams working across institutions and disciplines, and typically provides support to investigators working on computational phylogenetics and phyloinformatics tasks, including data acquisition, analysis, and algorithm development and dissemination.

Taxonomy—the classification, identification and naming of organisms—is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline.^[4] The degree to which taxonomies depend on phylogenies differs depending on the school of taxonomy: phenetics ignores phylogeny altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reproduce phylogeny in its classification without loss of information; evolutionary taxonomy tries to find a compromise between them in order to represent stages of evolution.

§Construction of a phylogenetic tree

The scientific methods of phylogenetics are often grouped under the term cladistics. The most common ones are parsimony, maximum likelihood (ML), and MCMC-based Bayesian inference. All methods depend upon an implicit or explicit mathematical model describing the evolution of characters observed in the species included; all can be, and are, used for molecular data, wherein the characters are aligned nucleotide or amino acid sequences, and all but maximum likelihood (see below) can be, and are, used for phenotypic (morphological, chemical, and physiological) data (also called classical or traditional data).

Phenetics, popular in the mid-20th century but now largely obsolete, uses distance matrix-based methods to construct trees based on overall similarity in morphology or other observable traits (i.e. in the phenotype, not the DNA), which was often assumed to approximate phylogenetic relationships.

A comprehensive step-by-step protocol on constructing phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test (testing best-fitting substitution models) and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference, is available at Nature Protocol^[5]

Prior to 1990, phylogenetic inferences were generally presented as narrative scenarios. Such methods are legitimate, but often ambiguous and hard to test.^[6][7][8]

§Limitations and workarounds

Ultimately, there is no way to measure whether a particular phylogenetic hypothesis is accurate or not, unless the true relationships among the taxa being examined are already known (which may happen with bacteria or viruses under laboratory conditions). The best result an empirical phylogeneticist can hope to attain is a tree with branches that are well supported by the available evidence. Several potential pitfalls have been identified:

§Homoplasy

Certain characters are more likely to evolve convergently than others; logically, such characters should be given less weight in the reconstruction of a tree.^[9] Weights in the form of a model of evolution can be inferred from sets of molecular data, so that maximum likelihood or Bayesian methods can be used to analyze them. For molecular sequences, this problem is exacerbated when the taxa under study have diverged substantially. As time since the divergence of two taxa increase, so does the probability of multiple substitutions on the same site, or back mutations, all of which result in homoplasies. For morphological data, unfortunately, the only objective way to determine convergence is by the construction of a tree – a somewhat circular method. Even so, weighting homoplasious characters^[how?] does indeed lead to better-supported trees.^[9] Further refinement can be brought by weighting changes in one direction higher than changes in another; for instance, the presence of thoracic wings almost guarantees placement among the pterygote insects because, although wings are often lost secondarily, there is no evidence that they have been gained more than once.^[10]

§Horizontal gene transfer

In general, organisms can inherit genes in two ways: vertical gene transfer and horizontal gene transfer. Vertical gene transfer is the passage of genes from parent to offspring, and horizontal (also called lateral) gene transfer occurs when genes jump between unrelated organisms, a common phenomenon especially in prokaryotes; a good example of this is the acquired antibiotic resistance as a result of gene exchange between various bacteria leading to multi-drug-resistant bacterial species. There have also been well-documented cases of horizontal gene transfer between eukaryotes.

Horizontal gene transfer has complicated the determination of phylogenies of organisms, and inconsistencies in phylogeny have been reported among specific groups of organisms depending on the genes used to construct evolutionary trees. The only way to determine which genes have been acquired vertically and which horizontally is to parsimoniously assume that the largest set of genes that have been inherited together have been inherited vertically; this requires analyzing a large number of genes.

§Taxon sampling

Owing to the development of advanced sequencing techniques in molecular biology, it has become feasible to gather large amounts of data (DNA or amino acid sequences) to infer phylogenetic hypotheses. For example, it is not rare to find studies with character matrices based on whole mitochondrial genomes (~16,000 nucleotides, in many animals). However, simulations have shown that it is more important to increase the number of taxa in the matrix than to increase the number of characters, because the more taxa there are, the more accurate and more robust is the resulting phylogenetic tree.^[11][12] This may be partly due to the breaking up of long branches.

§Phylogenetic signal

Another important factor that affects the accuracy of tree reconstruction is whether the data analyzed actually contain a useful phylogenetic signal, a term that is used generally to denote whether a character evolves slowly enough to have the same state in closely related taxa as opposed to varying randomly. Tests for phylogenetic signal exist.^[13]

§Continuous characters

Morphological characters that sample a continuum may contain phylogenetic signal, but are hard to code as discrete characters. Several methods have been used, one of which is gap coding, and there are variations on gap coding.^[14] In the original form of gap coding:^[14]

group means for a character are first ordered by size. The pooled within-group standard deviation is calculated … and differences between adjacent means … are compared relative to this standard deviation. Any pair of adjacent means is considered different and given different integer scores … if the means are separated by a "gap" greater than the within-group standard deviation … times some arbitrary constant.

If more taxa are added to the analysis, the gaps between taxa may become so small that all information is lost. Generalized gap coding works around that problem by comparing individual pairs of taxa rather than considering one set that contains all of the taxa.^[14]

§Missing data

In general, the more data that are available when constructing a tree, the more accurate and reliable the resulting tree will be. Missing data are no more detrimental than simply having fewer data, although the impact is greatest when most of the missing data are in a small number of taxa. Concentrating the missing data across a small number of characters produces a more robust tree.^[15]

§The role of fossils

Because many characters involve embryological, or soft-tissue or molecular characters that (at best) hardly ever fossilize, and the interpretation of fossils is more ambiguous than that of living taxa, extinct taxa almost invariably have higher proportions of missing data than living ones. However, despite these limitations, the inclusion of fossils is invaluable, as they can provide information in sparse areas of trees, breaking up long branches and constraining intermediate character states; thus, fossil taxa contribute as much to tree resolution as modern taxa.^[16] Fossils can also constrain the age of lineages and thus demonstrate how consistent a tree is with the stratigraphic record;^[17] stratocladistics incorporates age information into data matrices for phylogenetic analyses.

§History

The term "phylogeny" derives from the German Phylogenie, introduced by Haeckel in 1866.^[18]

§Ernst Haeckel's recapitulation theory

During the late 19th century, Ernst Haeckel's recapitulation theory, or "biogenetic fundamental law", was widely accepted. It was often expressed as "ontogeny recapitulates phylogeny", i.e. the development of an organism successively mirrors the adult stages of successive ancestors of the species to which it belongs. This theory has long been rejected.^[19][20] Instead, ontogeny evolves – the phylogenetic history of a species cannot be read directly from its ontogeny, as Haeckel thought would be possible, but characters from ontogeny can be (and have been) used as data for phylogenetic analyses; the more closely related two species are, the more apomorphies their embryos share.

§Timeline of key events

Branching tree diagram from Heinrich Georg Bronn'swork,(1858)

Phylogenetic tree suggested by Haeckel(1866)

• 1300s, lex parsimoniae (parsimony principle), William of Ockam, English philosopher, theologian, and Franciscan monk, but the idea actually goes back to Aristotle, precursor concept
• 1763, Bayesian probability, Rev. Thomas Bayes,^[21] precursor concept
• 1700s, Pierre Simon (Marquis de Laplace), perhaps 1st to use ML (maximum likelihood), precursor concept
• 1809, evolutionary theory, Philosophie Zoologique, Jean-Baptiste de Lamarck, precursor concept, foreshadowed in the 1600s and 1700s by Voltaire, Descartes, and Leibniz, with Leibniz even proposing evolutionary changes to account for observed gaps suggesting that many species had become extinct, others transformed, and different species that share common traits may have at one time been a single race,^[22] also foreshadowed by some early Greek philosophers such as Anaximander in the 6th century BC and the atomists of the 5th century BC, who proposed rudimentary theories of evolution^[23]
• 1837, Darwin's notebooks show an evolutionary tree^[24]
• 1843, distinction between homology and analogy (the latter now referred to as homoplasy), Richard Owen, precursor concept
• 1858, Paleontologist Heinrich Georg Bronn (1800–1862) published a hypothetical tree to illustrating the paleontological "arrival" of new, similar species following the extinction of an older species. Bronn did not propose a mechanism responsible for such phenomena, precursor concept.^[25]
• 1858, elaboration of evolutionary theory, Darwin and Wallace,^[26] also in Origin of Species by Darwin the following year, precursor concept
• 1866, Ernst Haeckel, first publishes his phylogeny-based evolutionary tree, precursor concept
• 1893, Dollo's Law of Character State Irreversibility,^[27] precursor concept
• 1912, ML recommended, analyzed, and popularized by Ronald Fisher, precursor concept
• 1921, Tillyard uses term "phylogenetic" and distinguishes between archaic and specialized characters in his classification system^[28]
• 1940, term "clade" coined by Lucien Cuénot
• 1949, jackknife, Maurice Quenouille (foreshadowed in '46 by Mahalanobis and extended in '58 by Tukey), precursor concept
• 1950, Willi Hennig's classic formalization^[29]
• 1952, William Wagner's groundplan divergence method^[30]
• 1953, "cladogenesis" coined^[31]
• 1960, "cladistic" coined by Cain and Harrison^[32]
• 1963, 1st attempt to use ML (maximum likelihood) for phylogenetics, Edwards and Cavalli-Sforza^[33]
• 1965
  • Camin-Sokal parsimony, 1st parsimony (optimization) criterion and 1st computer program/algorithm for cladistic analysis both by Camin and Sokal^[34]
  • character compatibility method, also called clique analysis, introduced independently by Camin and Sokal (loc. cit.) and E.O. Wilson^[35]
• 1966
  • English translation of Hennig^[36]
  • "cladistics" and "cladogram" coined (Webster's, loc. cit.)
• 1969
  • dynamic and successive weighting, James Farris^[37]
  • Wagner parsimony, Kluge and Farris^[38]
  • CI (consistency index), Kluge and Farris^[38]
  • introduction of pairwise compatibility for clique analysis, Le Quesne^[39]
• 1970, Wagner parsimony generalized by Farris^[40]
• 1971
  • Fitch parsimony, Fitch^[41]
  • NNI (nearest neighbour interchange), 1st branch-swapping search strategy, developed independently by Robinson^[42] and Moore et al.
  • ME (minimum evolution), Kidd and Sgaramella-Zonta^[43] (it is unclear if this is the pairwise distance method or related to ML as Edwards and Cavalli-Sforza call ML "minimum evolution".)
• 1972, Adams consensus, Adams^[44]
• 1974, 1st successful application of ML to phylogenetics (for nucleotide sequences), Neyman^[45]
• 1976, prefix system for ranks, Farris^[46]
• 1977, Dollo parsimony, Farris^[47]
• 1979
  • Nelson consensus, Nelson^[48]
  • MAST (maximum agreement subtree)((GAS)greatest agreement subtree), a consensus method, Gordon ^[49]
  • bootstrap, Bradley Efron, precursor concept^[50]
• 1980, PHYLIP, 1st software package for phylogenetic analysis, Felsenstein
• 1981
  • majority consensus, Margush and MacMorris^[51]
  • strict consensus, Sokal and Rohlf^[52]
  • 1st computationally efficient ML algorithm, Felsenstein^[53]
• 1982
  • PHYSIS, Mikevich and Farris
  • branch and bound, Hendy and Penny^[54]
• 1985
  • 1st cladistic analysis of eukaryotes based on combined phenotypic and genotypic evidence Diana Lipscomb^[55]
  • 1st issue of Cladistics
  • 1st phylogentic application of bootstrap, Felsenstein^[56]
  • 1st phylogenetic application of jackknife, Scott Lanyon^[57]
• 1986, MacClade, Maddison and Maddison
• 1987, neighbor-joining method Saitou and Nei^[58]
• 1988, Hennig86 (version 1.5), Farris
• 1989
  • RI (retention index), RCI (rescaled consistency index), Farris^[59]
  • HER (homoplasy excess ratio), Archie^[60]
• 1990
  • combinable components (semi-strict) consensus, Bremer^[61]
  • SPR (subtree pruning and regrafting), TBR (tree bisection and reconnection), Swofford and Olsen^[62]
• 1991
  • DDI (data decisiveness index), Goloboff^[63][64]
  • 1st cladistic analysis of eukaryotes based only on phenotypic evidence, Lipscomb
• 1993, implied weighting Goloboff^[65]
• 1994, Bremer support (decay index), Bremer^[66]
• 1994, reduced consensus: RCC (reduced cladistic consensus) for rooted trees, Wilkinson^[67]
• 1995, reduced consensus RPC (reduced partition consensus) for unrooted trees, Wilkinson^[68]
• 1996, 1st working methods for BI (Bayesian Inference)independently developed by Li,^[69] Mau,^[70] and Rannalla and Yang^[71] and all using MCMC (Markov chain-Monte Carlo)
• 1998, TNT (Tree Analysis Using New Technology), Goloboff, Farris, and Nixon
• 1999, Winclada, Nixon
• 2003, symmetrical resampling, Goloboff^[72]

Ontogeny

From Wikipedia, the free encyclopedia

The initial stages of human embryogenesis

Parts of a human embryo

This article concerns ontogeny in biology. Not to be confused with the philosophical concept ontology, or the medical terms oncology or odontology.

Ontogeny (also ontogenesis or morphogenesis) is the origination and development of an organism, usually from the time of fertilization of the egg to the organism's mature form. Yet, the term can be used to refer to the study of the entirety of an organism's lifespan.

Ontogeny pertains to the developmental history of an organism within its own lifetime, as distinct from phylogeny, which refers to the evolutionary history of a species. In practice, writers on evolution often speak of species as "developing" traits or characteristics. This can be misleading. While developmental (i.e., ontogenetic) processes can influence subsequent evolutionary (e.g., phylogenetic) processes^[1] (see evolutionary developmental biology), individual organisms develop (ontogeny), while species evolve (phylogeny).

Ontogeny, embryology and developmental biology are closely related studies and the terms are sometimes used interchangeably. Recently (2003), the term ontogeny has been used in cell biology to describe the development of various cell types within an organism.^[2]

Ontogeny is a useful field of study in many disciplines, including developmental biology, developmental psychology, developmental cognitive neuroscience, and developmental psychobiology.

Ontogeny is also a concept used in anthropology as "the process through which each of us embodies the history of our own making".^[3]

Etymology

The word ontogeny comes from the Greek ὄν, on (gen. ὄντος, ontos), i.e. "being; that which is", which is the present participle of the verb εἰμί, eimi, i.e. "to be, I am", and from the suffix -geny from the Greek -γένεια -geneia, which expresses the concept of "mode of production".^[4]

Nature and nurture

A seminal paper named ontogeny as one of the four primary questions of biology, along with Huxley's three others: causation, survival value and evolution.^[5] Tinbergen emphasized that the change of behavioral machinery during development was distinct from the change in behavior during development. "We can conclude that the thrush itself, i.e. its behavioral machinery, has changed only if the behavior change occurred while the environment was held constant...When we turn from description to causal analysis, and ask in what way the observed change in behavior machinery has been brought about, the natural first step is to try and distinguish between environmental influences and those within the animal...In ontogeny the conclusion that a certain change is internally controlled (is "innate") is reached by elimination. " (p. 424) Tinbergen was concerned that the elimination of environmental factors is difficult to establish, and the use of the word "innate" often misleading.

Ontogenetic allometry

Most organisms undergo dramatic changes in shape as they grow and mature. Even "reptiles" (e.g., crocodilians, turtles, snakes,^[6] lizards^[7]), in which the offspring are often viewed as miniature adults, show a variety of ontogenetic changes in morphology and physiology.^[8]

Anthropological application

Comparing ourselves to others is something humans do all the time. "In doing so we are acknowledging not so much our sameness to others or our difference, but rather the commonality that resides in our difference. In other words, because each one of us is at once remarkably similar to, and remarkably different from, all other humans, it makes little sense to think of comparison in terms of a list of absolute similarities and a list of absolute differences. Rather, in respect of all other humans, we find similarities in the ways we are different from one another and differences in the ways we are the same. That we are able to do this is a function of the genuinely historical process that is human ontogeny".^[3]

Sex

From Wikipedia, the free encyclopedia

The male gamete (sperm) fertilizing the female gamete (ovum)

Organisms of many species are specialized into male and female varieties, each known as a sex.^[1] Sexual reproduction involves the combining and mixing of genetic traits: specialized cells known as gametes combine to form offspring that inherit traits from each parent. Gametes can be identical in form and function (known as isogamy), but in many cases an asymmetry has evolved such that two sex-specific types of gametes (heterogametes) exist (known as anisogamy). By definition, male gametes are small, motile, and optimized to transport their genetic information over a distance, while female gametes are large, non-motile and contain the nutrients necessary for the early development of the young organism. Among humans and other mammals, males typically carry XY chromosomes, whereas females typically carry XX chromosomes, which are a part of the XY sex-determination system.

The gametes produced by an organism determine its sex: males produce male gametes (spermatozoa, or sperm, in animals; pollen in plants) while females produce female gametes (ova, or egg cells); individual organisms which produce both male and female gametes are termed hermaphroditic. Frequently, physical differences are associated with the different sexes of an organism; these sexual dimorphisms can reflect the different reproductive pressures the sexes experience.

Evolution

It is considered that sexual reproduction first appeared about a billion years ago, evolved within ancestral single-celled eukaryotes.^[2] The reason for the initial evolution of sex, and the reason(s) it has survived to the present, are still matters of debate. Some of the many plausible theories include: that sex creates variation among offspring, sex helps in the spread of advantageous traits, and that sex helps in the removal of disadvantageous traits.Sexual reproduction is a process specific to eukaryotes, organisms whose cells contain a nucleus and mitochondria. In addition to animals, plants, and fungi, other eukaryotes (e.g. the malaria parasite) also engage in sexual reproduction. Some bacteria use conjugation to transfer genetic material between cells; while not the same as sexual reproduction, this also results in the mixture of genetic traits.

What is considered defining of sexual reproduction in eukaryotes is the difference between the gametes and the binary nature of fertilization. Multiplicity of gamete types within a species would still be considered a form of sexual reproduction. However, no third gamete is known in multicellular animals.^[3][4][5]

While the evolution of sex itself dates to the prokaryote or early eukaryote stage, the origin of chromosomal sex determination may have been fairly early in eukaryotes. The ZW sex-determination system is shared by birds, some fish and some crustaceans. Most mammals, but also some insects (Drosophila) and plants (Ginkgo) use XY sex-determination. X0 sex-determination is found in certain insects.

No genes are shared between the avian ZW and mammal XY chromosomes,^[6] and from a comparison between chicken and human, the Z chromosome appeared similar to the autosomal chromosome 9 in human, rather than X or Y, suggesting that the ZW and XY sex-determination systems do not share an origin, but that the sex chromosomes are derived from autosomal chromosomes of the common ancestor of birds and mammals. A paper from 2004 compared the chicken Z chromosome with platypus X chromosomes and suggested that the two systems are related.^[7]

Sexual reproduction

The life cycle of sexually reproducing organisms cycles through haploid and diploid stages

Sexual reproduction in eukaryotes is a process whereby organisms form offspring that combine genetic traits from both parents. Chromosomes are passed on from one generation to the next in this process. Each cell in the offspring has half the chromosomes of the mother and half of the father.^[8] Genetic traits are contained within the deoxyribonucleic acid (DNA) of chromosomes—by combining one of each type of chromosomes from each parent, an organism is formed containing a doubled set of chromosomes. This double-chromosome stage is called "diploid", while the single-chromosome stage is "haploid". Diploid organisms can, in turn, form haploid cells (gametes) that randomly contain one of each of the chromosome pairs, via meiosis.^[9] Meiosis also involves a stage of chromosomal crossover, in which regions of DNA are exchanged between matched types of chromosomes, to form a new pair of mixed chromosomes. Crossing over and fertilization (the recombining of single sets of chromosomes to make a new diploid) result in the new organism containing a different set of genetic traits from either parent.

In many organisms, the haploid stage has been reduced to just gametes specialized to recombine and form a new diploid organism; in others, the gametes are capable of undergoing cell division to produce multicellular haploid organisms. In either case, gametes may be externally similar, particularly in size (isogamy), or may have evolved an asymmetry such that the gametes are different in size and other aspects (anisogamy).^[10] By convention, the larger gamete (called an ovum, or egg cell) is considered female, while the smaller gamete (called a spermatozoon, or sperm cell) is considered male. An individual that produces exclusively large gametes is female, and one that produces exclusively small gametes is male. An individual that produces both types of gametes is a hermaphrodite; in some cases hermaphrodites are able to self-fertilize and produce offspring on their own, without a second organism.^[11]

Animals

Hoverflies engaging in sexual intercourse

Most sexually reproducing animals spend their lives as diploid organisms, with the haploid stage reduced to single cell gametes.^[12] The gametes of animals have male and female forms—spermatozoa and egg cells. These gametes combine to form embryos which develop into a new organism.

The male gamete, a spermatozoon (produced within a testicle), is a small cell containing a single long flagellum which propels it.^[13] Spermatozoa are extremely reduced cells, lacking many cellular components that would be necessary for embryonic development. They are specialized for motility, seeking out an egg cell and fusing with it in a process called fertilization.

Female gametes are egg cells (produced within ovaries), large immobile cells that contain the nutrients and cellular components necessary for a developing embryo.^[14] Egg cells are often associated with other cells which support the development of the embryo, forming an egg. In mammals, the fertilized embryo instead develops within the female, receiving nutrition directly from its mother.

Animals are usually mobile and seek out a partner of the opposite sex for mating. Animals which live in the water can mate using external fertilization, where the eggs and sperm are released into and combine within the surrounding water.^[15] Most animals that live outside of water, however, must transfer sperm from male to female to achieve internal fertilization.

In most birds, both excretion and reproduction is done through a single posterior opening, called the cloaca—male and female birds touch cloaca to transfer sperm, a process called "cloacal kissing".^[16] In many other terrestrial animals, males use specialized sex organs to assist the transport of sperm—these male sex organs are called intromittent organs. In humans and other mammals this male organ is the penis, which enters the female reproductive tract (called the vagina) to achieve insemination—a process called sexual intercourse. The penis contains a tube through which semen (a fluid containing sperm) travels. In female mammals the vagina connects with the uterus, an organ which directly supports the development of a fertilized embryo within (a process called gestation).

Because of their motility, animal sexual behavior can involve coercive sex. Traumatic insemination, for example, is used by some insect species to inseminate females through a wound in the abdominal cavity – a process detrimental to the female's health.

Plants

Flowers are the sexual organs of flowering plants, usually containing both male and female parts.

Like animals, plants have developed specialized male and female gametes.^[17] Within most familiar plants, male gametes are contained within hard coats, forming pollen. The female gametes of plants are contained within ovules; once fertilized by pollen these form seeds which, like eggs, contain the nutrients necessary for the development of the embryonic plant.

Female (left) and male (right) cones are the sex organs of pines and other conifers.

Many plants have flowers and these are the sexual organs of those plants. Flowers are usually hermaphroditic, producing both male and female gametes. The female parts, in the center of a flower, are the carpels—one or more of these may be merged to form a single pistil. Within carpels are ovules which develop into seeds after fertilization. The male parts of the flower are the stamens: these long filamentous organs are arranged between the pistil and the petals and produce pollen at their tips. When a pollen grain lands upon the top of a carpel, the tissues of the plant react to transport the grain down into the carpel to merge with an ovule, eventually forming seeds.

In pines and other conifers the sex organs are conifer cones and have male and female forms. The more familiar female cones are typically more durable, containing ovules within them. Male cones are smaller and produce pollen which is transported by wind to land in female cones. As with flowers, seeds form within the female cone after pollination.

Because plants are immobile, they depend upon passive methods for transporting pollen grains to other plants. Many plants, including conifers and grasses, produce lightweight pollen which is carried by wind to neighboring plants. Other plants have heavier, sticky pollen that is specialized for transportation by insects. The plants attract these insects with nectar-containing flowers. Insects transport the pollen as they move to other flowers, which also contain female reproductive organs, resulting in pollination.

Fungi

Mushrooms are produced as part of fungal sexual reproduction

Most fungi reproduce sexually, having both a haploid and diploid stage in their life cycles. These fungi are typically isogamous, lacking male and female specialization: haploid fungi grow into contact with each other and then fuse their cells. In some of these cases the fusion is asymmetric, and the cell which donates only a nucleus (and not accompanying cellular material) could arguably be considered "male".^[18]

Some fungi, including baker's yeast, have mating types that create a duality similar to male and female roles. Yeast with the same mating type will not fuse with each other to form diploid cells, only with yeast carrying the other mating type.^[19]

Fungi produce mushrooms as part of their sexual reproduction. Within the mushroom diploid cells are formed, later dividing into haploid spores—the height of the mushroom aids the dispersal of these sexually produced offspring.

Sex determination

Sex helps the spread of advantageous traits through recombination. The diagrams compare evolution of allele frequency in a sexual population (top) and an asexual population (bottom). The vertical axis shows frequency and the horizontal axis shows time. The alleles a/A and b/B occur at random. The advantageous alleles A and B, arising independently, can be rapidly combined by sexual reproduction into the most advantageous combination AB. Asexual reproduction takes longer to achieve this combination, because it can only produce AB if A arises in an individual which already has B, or vice versa.

The most basic sexual system is one in which all organisms are hermaphrodites, producing both male and female gametes—this is true of some animals (e.g. snails) and the majority of flowering plants.^[20] In many cases, however, specialization of sex has evolved such that some organisms produce only male or only female gametes. The biological cause for an organism developing into one sex or the other is called sex determination.

In the majority of species with sex specialization, organisms are either male (producing only male gametes) or female (producing only female gametes). Exceptions are common—for example, in the roundworm C. elegans the two sexes are hermaphrodite and male (a system called androdioecy).

Sometimes an organism's development is intermediate between male and female, a condition called intersex. Sometimes intersex individuals are called "hermaphrodite"; but, unlike biological hermaphrodites, intersex individuals are unusual cases and are not typically fertile in both male and female aspects.

Genetic

Like humans and other mammals, the common fruit fly has an XY sex-determination system.

In genetic sex-determination systems, an organism's sex is determined by the genome it inherits. Genetic sex-determination usually depends on asymmetrically inherited sex chromosomes which carry genetic features that influence development; sex may be determined either by the presence of a sex chromosome or by how many the organism has. Genetic sex-determination, because it is determined by chromosome assortment, usually results in a 1:1 ratio of male and female offspring.

Humans and other mammals have an XY sex-determination system: the Y chromosome carries factors responsible for triggering male development. The default sex, in the absence of a Y chromosome, is female. Thus, XX mammals are female and XY are male. XY sex determination is found in other organisms, including the common fruit fly and some plants.^[20] In some cases, including in the fruit fly, it is the number of X chromosomes that determines sex rather than the presence of a Y chromosome (see below).

In birds, which have a ZW sex-determination system, the opposite is true: the W chromosome carries factors responsible for female development, and default development is male.^[21] In this case ZZ individuals are male and ZW are female. The majority of butterflies and moths also have a ZW sex-determination system. In both XY and ZW sex determination systems, the sex chromosome carrying the critical factors is often significantly smaller, carrying little more than the genes necessary for triggering the development of a given sex.^[22]

Many insects use a sex determination system based on the number of sex chromosomes. This is called X0 sex-determination—the 0 indicates the absence of the sex chromosome. All other chromosomes in these organisms are diploid, but organisms may inherit one or two X chromosomes. In field crickets, for example, insects with a single X chromosome develop as male, while those with two develop as female.^[23] In the nematode C. elegans most worms are self-fertilizing XX hermaphrodites, but occasionally abnormalities in chromosome inheritance regularly give rise to individuals with only one X chromosome—these X0 individuals are fertile males (and half their offspring are male).^[24]

Other insects, including honey bees and ants, use a haplodiploid sex-determination system.^[25] In this case diploid individuals are generally female, and haploid individuals (which develop from unfertilized eggs) are male. This sex-determination system results in highly biased sex ratios, as the sex of offspring is determined by fertilization rather than the assortment of chromosomes during meiosis.

Nongenetic

Clownfish are initially male; the largest fish in a group becomes female

For many species, sex is not determined by inherited traits, but instead by environmental factors experienced during development or later in life. Many reptiles have temperature-dependent sex determination: the temperature embryos experience during their development determines the sex of the organism. In some turtles, for example, males are produced at lower incubation temperatures than females; this difference in critical temperatures can be as little as 1–2 °C.

Many fish change sex over the course of their lifespan, a phenomenon called sequential hermaphroditism. In clownfish, smaller fish are male, and the dominant and largest fish in a group becomes female. In many wrasses the opposite is true—most fish are initially female and become male when they reach a certain size. Sequential hermaphrodites may produce both types of gametes over the course of their lifetime, but at any given point they are either female or male.

In some ferns the default sex is hermaphrodite, but ferns which grow in soil that has previously supported hermaphrodites are influenced by residual hormones to instead develop as male.^[26]

Sexual dimorphism

Common Pheasants are sexually dimorphic in both size and appearance.

Many animals and some plants have differences between the male and female sexes in size and appearance, a phenomenon called sexual dimorphism. Sex differences in humans include, generally, a larger size and more body hair in men; women have breasts, wider hips, and a higher body fat percentage. In other species, the differences may be more extreme, such as differences in coloration or bodyweight. In humans, biological sex is determined by five factors present at birth: the presence or absence of a Y chromosome, the type of gonads, the sex hormones, the internal reproductive anatomy (such as the uterus in females), and the external genitalia.^[27]

Sexual dimorphisms in animals are often associated with sexual selection – the competition between individuals of one sex to mate with the opposite sex.^[28] Antlers in male deer, for example, are used in combat between males to win reproductive access to female deer. In many cases the male of a species is larger than the female. Mammal species with extreme sexual size dimorphism tend to have highly polygynous mating systems—presumably due to selection for success in competition with other males—such as the elephant seals. Other examples demonstrate that it is the preference of females that drive sexual dimorphism, such as in the case of the stalk-eyed fly.^[29]

Other animals, including most insects and many fish, have larger females. This may be associated with the cost of producing egg cells, which requires more nutrition than producing sperm—larger females are able to produce more eggs.^[30] For example, female southern black widow spiders are typically twice as long as the males.^[31] Occasionally this dimorphism is extreme, with males reduced to living as parasites dependent on the female, such as in the anglerfish. Some plant species also exhibit dimorphism in which the females are significantly larger than the males, such as in the moss Dicranum^[32] and the liverwort Sphaerocarpos.^[33] There is some evidence that, in these genera, the dimorphism may be tied to a sex chromosome,^[33][34] or to chemical signalling from females.^[35]

In birds, males often have a more colourful appearance and may have features (like the long tail of male peacocks) that would seem to put the organism at a disadvantage (e.g. bright colors would seem to make a bird more visible to predators). One proposed explanation for this is the handicap principle.^[36] This hypothesis says that, by demonstrating he can survive with such handicaps, the male is advertising his genetic fitness to females—traits that will benefit daughters as well, who will not be encumbered with such handicaps.

Birth

From Wikipedia, the free encyclopedia

Lambing: the mother licks the first lamb while giving birth to the second

Birth, also known as parturition, is the act or process of bearing or bringing forth offspring.^[1] In mammals, the process is initiated by hormones which cause the muscular walls of the uterus to contract, expelling the fetus at a developmental stage when it is ready to feed and breathe. In some species the offspring is precocial and can move around almost immediately after birth but in others it is altricial and completely dependent on parenting. In marsupials, the fetus is born at a very immature stage after a short gestational period and develops further in its mother's pouch.

It is not only mammals that give birth. Some reptiles, amphibians, fish and invertebrates carry their developing young inside them. Some of these are ovoviviparous, with the eggs being hatched inside the mother's body, and others are viviparous, with the embryo developing inside her body, as in mammals.

Birth in mammals

Large mammals, such as primates, cattle, horses, some antelopes, giraffes, hippopotamuses, rhinoceroses, elephants, seals, whales, dolphins, and porpoises, generally are pregnant with one offspring at a time; although, they may have twin or multiple births on occasion. In these large animals, the birth process is similar to that of a human though in most, the offspring is precocial. This means that it is born in a more advanced state than a human baby and is able to stand, walk and run (or swim in the case of an aquatic mammal) shortly after birth.^[2] In the case of whales, dolphins and porpoises, the single calf is normally born tail first which minimises the risk of drowning.^[3] The mother encourages the newborn calf to rise to the surface of the water to breathe.^[4]

Most smaller mammals have multiple births, producing litters of young which may number twelve or more. In these animals, each fetus is surrounded by its own amniotic sac and has a separate placenta. This separates from the wall of the uterus during labor and the fetus works its way towards the birth canal.^{[citation needed]}

Human birth

An illustration of normal head-first presentation by the obstetrician William Smellie from about 1792. The membranes have ruptured and the cervix is fully dilated.

Humans usually produce a single offspring at a time. The mother's body is prepared for birth by hormones produced by the pituitary gland, the ovary and the placenta.^[2] The total gestation period from fertilization to birth is normally about 38 weeks (birth usually occurring 40 weeks after the last menstrual period). The normal process of childbirth takes several hours and has three stages. The first stage starts with a series of involuntary contractions of the muscular walls of the uterus and gradual dilation of the cervix. The active phase of the first stage starts when the cervix is dilated more than about 4 cm in diameter and is when the contractions become stronger and regular. The head (or the buttocks in a breech birth) of the baby is pushed against the cervix, which gradually dilates until is fully dilated at 10 cm diameter. At some time, the amniotic sac bursts and the amniotic fluid escapes (also known as rupture of membranes or breaking the water).^[5] In stage two, starting when the cervix is fully dilated, strong contractions of the uterus and active pushing by the mother expels the baby out through the vagina, which during this stage of labour is called a birth canal as this passage contains a baby, and the baby is born with umbilical cord attached.^[6] In stage three, which begins after the birth of the baby, further contractions expel the placenta, amniotic sac, and the remaining portion of the umbilical cord usually within a few minutes.^[7]

Enormous changes take place in the newborn's circulation to enable breathing in air. In the uterus, the unborn baby is dependent on circulation of blood through the placenta for sustenance including gaseous exchange and the unborn baby's blood bypasses the lungs by flowing though the foramen ovale, which is a hole in the septum dividing the right atrium and left atrium. After birth the umbilical cord is clamped and cut, the baby starts to breathe air, and blood from the right ventricle starts to flow to the lungs for gaseous exchange and oxygenated blood returns to the left atrium, which is pumped into the left ventricle, and then pumped into the main arterial system. As result of these changes, the blood pressure in the left atrium exceeds the pressure in the right atrium, and this pressure difference forces the foramen ovale to close separating the left and right sides of the heart. The umbilical vein, umbilical arteries, ductus venosus and ductus arteriosus are not needed for life in air and in time these vessels become ligaments (embryonic remnants).^[8]

Cattle

Cow and newborn calf

Birthing in cattle is typical of a larger mammal. A cow goes through three stages of labor during normal delivery of a calf. During stage one, the animal seeks a quiet place away from the rest of the herd. Hormone changes cause soft tissues of the birth canal to relax as the mother's body prepares for birth. The contractions of the uterus are not obvious externally, but the cow may be restless. She may appear agitated, alternating between standing and lying down, with her tail slightly raised and her back arched. The fetus is pushed toward the birth canal by each contraction and the cow's cervix gradually begins to dilate. Stage one may last several hours, and ends when the cervix is fully dilated. Stage two can be seen to be underway when there is external protrusion of the amniotic sac through the vulva, closely followed by the appearance of the calf's front hooves and head in a front presentation (or occasionally the calf's tail and rear end in a posterior presentation).^[9] During the second stage, the cow will usually lie down on her side to push and the calf progresses through the birth canal. The complete delivery of the calf (or calves in a multiple birth) signifies the end of stage two. The cow scrambles to her feet (if lying down at this stage), turns round and starts vigorously licking the calf. The calf takes its first few breaths and within minutes is struggling to rise to its feet. The third and final stage of labor is the delivery of the placenta, which is usually expelled within a few hours and is often eaten by the normally herbivorous cow.^[9][10]

Dogs

In the dog, as birth approaches, contractions become more frequent. The amniotic sac looking like a glistening grey balloon, with a puppy inside, is propelled through the vulva. After further contractions, the sac is expelled and the bitch breaks the membranes releasing clear fluid and exposing the puppy. The mother chews at the umbilical cord and licks the puppy vigorously, which stimulates it to breathe. If the puppy has not taken its first breath within about six minutes, it is likely to die. Further puppies follow in a similar way one by one usually with less straining than the first. The mother will then usually eat the afterbirth.^[11]

Marsupials

A kangaroo joey firmly attached to a nipple inside the pouch

An infant marsupial is born in a very immature state. The gestation period is usually shorter than the intervals between oestrus periods. During gestation there is no placenta but the fetus is contained in a little yellow sac and feeds on a yolk. The first sign that a birth is imminent is the mother cleaning out her pouch. When it is born, the infant is pink, blind, furless and a few centimetres long. It has nostrils in order to breathe and forelegs to cling onto its mother's hairs but its hind legs are undeveloped. It crawls through its mother's fur and makes its way into the pouch. Here it fixes onto a teat which swells inside its mouth. It stays attached to the teat for several months until it is sufficiently developed to emerge.^[12]

Birth in other animals

The vast majority of invertebrates, most fish, reptiles and amphibians and all birds are oviparous, that is, they lay eggs with little or no embryonic development taking place within the mother. In aquatic organisms, fertilization is nearly always external with sperm and eggs being liberated into the water (an exception is sharks and rays, which have internal fertilization^[13]). Millions of eggs may be produced with no further parental involvement, in the expectation that a small number may survive to become mature individuals. Terrestrial invertebrates may also produce large numbers of eggs, a few of which may avoid predation and carry on the species. Some fish, reptiles and amphibians have adopted a different strategy and invest their effort in producing a small number of young at a more advanced stage which are more likely to survive to adulthood. Birds care for their young in the nest and provide for their needs after hatching and it is perhaps unsurprising that internal development does not occur in birds, given their need to fly.^[14]

Ovoviviparity is a mode of reproduction in which embryos develop inside eggs that remain in the mother's body until they are ready to hatch. Ovoviviparous animals are similar to viviparous species in that there is internal fertilization and the young are born in an advanced state, but differ in that there is no placental connection and the unborn young are nourished by egg yolk. The mother's body provides gas exchange (respiration), but that is largely necessary for oviparous animals as well.^[14] In many sharks the eggs hatch in the oviduct within the mother's body and the embryos are nourished by the egg's yolk and fluids secreted by glands in the walls of the oviduct. The Lamniforme sharks practice oophagy, where the first embryos to hatch consume the remaining eggs and sand tiger shark pups cannibalistically consume neighbouring embryos. The requiem sharks maintain a placental link to the developing young, this practice is known as viviparity. This is more analogous to mammalian gestation than to that of other fishes. In all these cases, the young are born alive and fully functional.^[15] The majority of caecilians are oviviviparous and give birth to already developed offspring. When the young have finished their yolk sacs they feed on nutrients secreted by cells lining the oviduct and even the cells themselves which they eat with specialist scraping teeth.^[16] The Alpine salamander (Salamandra atra) and several species of Tanzanian toad in the genus Nectophrynoides are oviviviparous, developing through the larval stage inside the mother's oviduct and eventually emerging as fully formed juveniles.^[17]

A more developed form of vivipary called placental viviparity is adopted by some species of scorpions^[18] and cockroaches,^[19] certain genera of sharks, snakes and velvet worms. In these, the developing embryo is nourished by some form of placental structure. The earliest known placenta was found recently in a group of extinct fishes called placoderms, which are ancestral to mammals. A fossil from Australia's Gogo Formation, laid down in the Devonian period, 380 million years ago, was found with an embryo inside it connected by an umbilical cord to a yolk sac. The find confirmed the hypothesis that a sub-group of placoderms, called ptyctodontids, fertilized their eggs internally. Some fishes that fertilize their eggs internally also give birth to live young, as seen here. This discovery moved our knowledge of live birth back 200 million years.^[20] The fossil of another genus was found with three embryos in the same position.^[21] Placoderms are a sister group of the ancestor of all living jawed fishes (Gnathostomata), including both chondrichthyians, the sharks & rays, and Osteichthyes, the bony fishes.

Among lizards, the viviparous lizard Zootoca vivipara, slow worms and many species of skink are viviparous, giving birth to live young. Some are ovoviviparous but others such as members of the genera Tiliqua and Corucia, give birth to live young that develop internally, deriving their nourishment from a mammal-like placenta attached to the inside of the mother's uterus. In a recently described example, an African species, Trachylepis ivensi, has developed a purely reptilian placenta directly comparable in structure and function to a mammalian placenta.^[22] Vivipary is rare in snakes, but boas and vipers are viviparous, giving birth to live young.

Female aphid giving birth

The majority of insects lay eggs but a very few give birth to offspring that are miniature versions of the adult.^[14] The aphid has a complex life cycle and during the summer months is able to multiply with great rapidity. Its reproduction is typically parthenogenetic and viviparous and females produce unfertilized eggs which they retain within their bodies.^[23] The embryos develop within their mothers' ovarioles and the offspring are clones of their mothers. Female nymphs are born which grow rapidly and soon produce more female offspring themselves.^[24] In some instances, the newborn nymphs already have developing embryos inside them.^[14]