2.4: Perspectives on the Phylogenetic Tree - Biology

2.4: Perspectives on the Phylogenetic Tree - Biology

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Learning Objectives

  • Describe horizontal gene transfer.
  • Illustrate how prokaryotes and eukaryotes transfer genes horizontally.
  • Describe the process of endosymbiosis and explain how this can produce membrane-bound organelles.
  • Identify the web and ring models of phylogenetic relationships and describe how they differ from the original phylogenetic tree concept.

The concepts of phylogenetic modeling are constantly changing. Over the last several decades, new research has challenged scientists’ ideas about how organisms are related. New models of these relationships have been proposed for consideration by the scientific community.

Many phylogenetic trees have been shown as models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 (Figure (PageIndex{1})a), which served as a pattern for subsequent studies for more than a century. The concept of a phylogenetic tree with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the structure of many common trees, such as the oak ((PageIndex{a})b). However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the validity of the standard tree model in the scientific community.

Limitations to the Classic Model

Classical thinking about prokaryotic evolution, included in the classic tree model, is that species evolve clonaly. That is, they produce offspring themselves with only random mutations causing the descent into the variety of modern-day and extinct species known to science. This view is somewhat complicated in eukaryotes that reproduce sexually, but the laws of Mendelian genetics explain the variation in offspring, again, to be a result of a mutation within the species. The concept of genes being transferred between unrelated species was not considered as a possibility until relatively recently. Horizontal gene transfer (HGT), also known as lateral gene transfer, is the transfer of genes between unrelated species. HGT has been shown to be an ever-present phenomenon, with many evolutionists postulating a major role for this process in evolution, thus complicating the simple tree model. Genes have been shown to be passed between species which are only distantly related using standard phylogeny, thus adding a layer of complexity to the understanding of phylogenetic relationships.

The various ways that HGT occurs in prokaryotes is important to understanding phylogenies. Although at present HGT is not viewed as important to eukaryotic evolution, HGT does occur in this domain as well. Finally, as an example of the ultimate gene transfer, theories of genome fusion between symbiotic or endosymbiotic organisms have been proposed to explain an event of great importance—the evolution of the first eukaryotic cell, without which humans could not have come into existence.

Horizontal Gene Transfer

Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring. These transfers allow even distantly related species to share genes, influencing their phenotypes. It is thought that HGT is more prevalent in prokaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process. Some researchers believe such estimates are premature: the actual importance of HGT to evolutionary processes must be viewed as a work in progress. As the phenomenon is investigated more thoroughly, it may be revealed to be more common. Many scientists believe that HGT and mutation appear to be (especially in prokaryotes) a significant source of genetic variation, which is the raw material for the process of natural selection. These transfers may occur between any two species that share an intimate relationship (Table (PageIndex{1})).

Table (PageIndex{1}): Summary of Mechanisms of Prokaryotic and Eukaryotic HGT.

MechanismMode of TransmissionExample
ProkaryotestransformationDNA uptakemany prokaryotes
transductionbacteriophage (virus)bacteria
conjugationpilusmany prokaryotes
gene transfer agentsphage-like particlespurple non-sulfur bacteria
Eukaryotesfrom food organismsunknownaphid
jumping genestransposonsrice and millet plants
epiphytes/parasitesunknownyew tree fungi
from viral infections

HGT in Prokaryotes

The mechanism of HGT has been shown to be quite common in the prokaryotic domains of Bacteria and Archaea, significantly changing the way their evolution is viewed. The majority of evolutionary models, such as in the Endosymbiotic Theory, propose that eukaryotes descended from multiple prokaryotes, which makes HGT all the more important to understanding the phylogenetic relationships of all extant and extinct species.

The fact that genes are transferred among common bacteria is well known to microbiology students. These gene transfers between species are the major mechanism whereby bacteria acquire resistance to antibiotics. Classically, this type of transfer has been thought to occur by three different mechanisms:

  1. Transformation: naked DNA is taken up by a bacteria
  2. Transduction: genes are transferred using a virus
  3. Conjugation: the use a hollow tube called a pilus to transfer genes between organisms

More recently, a fourth mechanism of gene transfer between prokaryotes has been discovered. Small, virus-like particles called gene transfer agents (GTAs) transfer random genomic segments from one species of prokaryote to another. GTAs have been shown to be responsible for genetic changes, sometimes at a very high frequency compared to other evolutionary processes. The first GTA was characterized in 1974 using purple, non-sulfur bacteria. These GTAs, which are thought to be bacteriophages (viruses that infect bacteria) that lost the ability to reproduce on their own, carry random pieces of DNA from one organism to another. The ability of GTAs to act with high frequency has been demonstrated in controlled studies using marine bacteria. Gene transfer events in marine prokaryotes, either by GTAs or by viruses, have been estimated to be as high as 1013 per year in the Mediterranean Sea alone. GTAs and viruses are thought to be efficient HGT vehicles with a major impact on prokaryotic evolution.

As a consequence of this modern DNA analysis, the idea that eukaryotes evolved directly from Archaea has fallen out of favor. While eukaryotes share many features that are absent in bacteria, such as the TATA box (found in the promoter region of many genes), the discovery that some eukaryotic genes were more homologous with bacterial DNA than Archaea DNA made this idea less tenable. Furthermore, the fusion of genomes from Archaea and Bacteria by endosymbiosis has been proposed as the ultimate event in eukaryotic evolution.

HGT in Eukaryotes

Although it is easy to see how prokaryotes exchange genetic material by HGT, it was initially thought that this process was absent in eukaryotes. After all, prokaryotes are but single cells exposed directly to their environment, whereas the sex cells of multicellular organisms are usually sequestered in protected parts of the body. It follows from this idea that the gene transfers between multicellular eukaryotes should be more difficult. Indeed, it is thought that this process is rarer in eukaryotes and has a much smaller evolutionary impact than in prokaryotes. In spite of this fact, HGT between distantly related organisms has been demonstrated in several eukaryotic species, and it is possible that more examples will be discovered in the future.

In plants, gene transfer has been observed in species that cannot cross-pollinate by normal means. Transposons or “jumping genes” have been shown to transfer between rice and millet plant species. Furthermore, fungal species feeding on yew trees, from which the anti-cancer drug TAXOL® is derived from the bark, have acquired the ability to make taxol themselves, a clear example of gene transfer.

In animals, a particularly interesting example of HGT occurs within the aphid species (Figure (PageIndex{2})). Aphids are insects that vary in color based on carotenoid content. Carotenoids are pigments made by a variety of plants, fungi, and microbes, and they serve a variety of functions in animals, who obtain these chemicals from their food. Humans require carotenoids to synthesize vitamin A, and we obtain them by eating orange fruits and vegetables: carrots, apricots, mangoes, and sweet potatoes. On the other hand, aphids have acquired the ability to make the carotenoids on their own. According to DNA analysis, this ability is due to the transfer of fungal genes into the insect by HGT, presumably as the insect consumed fungi for food. A carotenoid enzyme called a desaturase is responsible for the red coloration seen in certain aphids, and it has been further shown that when this gene is inactivated by mutation, the aphids revert back to their more common green color (Figure (PageIndex{2})).

Endosymbiosis, Genome Fusion, and the Evolution of Eukaryotes

Scientists believe the ultimate in HGT occurs through genome fusion between different species of prokaryotes when two symbiotic organisms become endosymbiotic. This occurs when one species is taken inside the cytoplasm of another species (see Figure (PageIndex{3})), which ultimately results in a genome consisting of genes from both the endosymbiont and the host. This mechanism is an aspect of the Endosymbiont Theory, which is accepted by a majority of biologists as the mechanism whereby eukaryotic cells obtained their mitochondria and chloroplasts. However, the role of endosymbiosis in the development of the nucleus is more controversial. Nuclear and mitochondrial DNA are thought to be of different (separate) evolutionary origin, with the mitochondrial DNA being derived from the circular genomes of bacteria that were engulfed by ancient prokaryotic cells. Mitochondrial DNA can be regarded as the smallest chromosome. Mitochondrial DNA is usually inherited from the mother only. The mitochondrial DNA degrades in sperm when the sperm degrades in the fertilized egg or in other instances when the mitochondria located in the flagellum of the sperm fails to enter the egg. However, recent studies suggest fathers also occasionally contribute their mitochondrial DNA to their offspring as well (See Nature Article)

Within the past decade, the process of genome fusion by endosymbiosis has been proposed by James Lake of the UCLA/NASA Astrobiology Institute to be responsible for the evolution of the first eukaryotic cells (Figure (PageIndex{4})a). Using DNA analysis and a new mathematical algorithm called conditioned reconstruction (CR), his laboratory proposed that eukaryotic cells developed from an endosymbiotic gene fusion between two species, one an Archaea and the other a Bacteria. As mentioned, some eukaryotic genes resemble those of Archaea, whereas others resemble those from Bacteria. An endosymbiotic fusion event, such as Lake has proposed, would clearly explain this observation. On the other hand, this work is new and the CR algorithm is relatively unsubstantiated, which causes many scientists to resist this hypothesis.

More recent work by Lake ((PageIndex{d})b) proposes that gram-negative bacteria, which are unique within their domain in that they contain two lipid bilayer membranes, indeed resulted from an endosymbiotic fusion of archaeal and bacterial species. The double membrane would be a direct result of the endosymbiosis, with the endosymbiont picking up the second membrane from the host as it was internalized. This mechanism has also been used to explain the double membranes found in mitochondria and chloroplasts. Lake’s work is not without skepticism, and the ideas are still debated within the biological science community. In addition to Lake’s hypothesis, there are several other competing theories as to the origin of eukaryotes. How did the eukaryotic nucleus evolve? One theory is that the prokaryotic cells produced an additional membrane that surrounded the bacterial chromosome. Some bacteria have the DNA enclosed by two membranes; however, there is no evidence of a nucleolus or nuclear pores. Other proteobacteria also have membrane-bound chromosomes. If the eukaryotic nucleus evolved this way, we would expect one of the two types of prokaryotes to be more closely related to eukaryotes.

The nucleus-first hypothesis proposes that the nucleus evolved in prokaryotes first ((PageIndex{e})a), followed by a later fusion of the new eukaryote with bacteria that became mitochondria. The mitochondria-first hypothesis proposes that mitochondria were first established in a prokaryotic host ((PageIndex{e})b), which subsequently acquired a nucleus, by fusion or other mechanisms, to become the first eukaryotic cell. Most interestingly, the eukaryote-first hypothesis proposes that prokaryotes actually evolved from eukaryotes by losing genes and complexity ((PageIndex{e})c). All of these hypotheses are testable. Only time and more experimentation will determine which hypothesis is best supported by data.

Web and Network Models

The recognition of the importance of HGT, especially in the evolution of prokaryotes, has caused some to propose abandoning the classic “tree of life” model. In 1999, W. Ford Doolittle proposed a phylogenetic model that resembles a web or a network more than a tree. The hypothesis is that eukaryotes evolved not from a single prokaryotic ancestor, but from a pool of many species that were sharing genes by HGT mechanisms. As shown in Figure (PageIndex{6})a, some individual prokaryotes were responsible for transferring the bacteria that caused mitochondrial development to the new eukaryotes, whereas other species transferred the bacteria that gave rise to chloroplasts. This model is often called the “web of life.” In an effort to save the tree analogy, some have proposed using the Ficus tree (Figure (PageIndex{6})b) with its multiple trunks as a phylogenetic to represent a diminished evolutionary role for HGT.

Ring of Life Models

Others have proposed abandoning any tree-like model of phylogeny in favor of a ring structure, the so-called “ring of life” (Figure (PageIndex{7})); a phylogenetic model where all three domains of life evolved from a pool of primitive prokaryotes. Lake, again using the conditioned reconstruction algorithm, proposes a ring-like model in which species of all three domains—Archaea, Bacteria, and Eukarya—evolved from a single pool of gene-swapping prokaryotes. His laboratory proposes that this structure is the best fit for data from extensive DNA analyses performed in his laboratory, and that the ring model is the only one that adequately takes HGT and genomic fusion into account. However, other phylogeneticists remain highly skeptical of this model.

In summary, the “tree of life” model proposed by Darwin must be modified to include HGT. Does this mean abandoning the tree model completely? Even Lake argues that all attempts should be made to discover some modification of the tree model to allow it to accurately fit his data, and only the inability to do so will sway people toward his ring proposal.

This doesn’t mean a tree, web, or a ring will correlate completely to an accurate description of phylogenetic relationships of life. A consequence of the new thinking about phylogenetic models is the idea that Darwin’s original conception of the phylogenetic tree is too simple, but made sense based on what was known at the time. However, the search for a more useful model moves on: each model serving as hypotheses to be tested with the possibility of developing new models. This is how science advances. These models are used as visualizations to help construct hypothetical evolutionary relationships and understand the massive amount of data being analyzed.


The phylogenetic tree, first used by Darwin, is the classic “tree of life” model describing phylogenetic relationships among species, and the most common model used today. New ideas about HGT and genome fusion have caused some to suggest revising the model to resemble webs or rings.

Perspectives On the Phylogenetic Tree

The concepts of phylogenetic modeling are constantly changing. It is one of the most dynamic fields of study in all of biology. Over the last several decades, new research has challenged scientists’ ideas about how organisms are related. New models of these relationships have been proposed for consideration by the scientific community.

Many phylogenetic trees have been shown as models of the evolutionary relationship among species. Phylogenetic trees originated with Charles Darwin, who sketched the first phylogenetic tree in 1837 (figure (a) below), which served as a pattern for subsequent studies for more than a century.

The concept of a phylogenetic tree with a single trunk representing a common ancestor, with the branches representing the divergence of species from this ancestor, fits well with the structure of many common trees, such as the oak (figure (b) below). However, evidence from modern DNA sequence analysis and newly developed computer algorithms has caused skepticism about the validity of the standard tree model in the scientific community.

The (a) concept of the “tree of life” goes back to an 1837 sketch by Charles Darwin. Like an (b) oak tree, the “tree of life” has a single trunk and many branches. (credit b: modification of work by “Amada44″/Wikimedia Commons)


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Generating a Molecular Sequence Matrix

The issue of which traits to use for phylogenetic analysis has been the subject of much discussion. For example, there has been a running debate in the field of vertebrate evolution regarding the value of morphological character traits versus molecular traits. Although these debates can catalyze discussion of important issues, we believe that the &ldquoeither/or&rdquo division that they sometimes imply is spurious. Instead, what is needed is a case-by-case evaluation using objective and relevant criteria, such as cost, accuracy of character state assignment, ease of inferring homology, lack of convergent evolution, number of possible character states and rate of change between them, and utility of the character information for other purposes.

For instructional purposes, the remainder of this chapter focuses on using molecular sequence data for phylogenetic reconstruction. This is not to say that such data are better or worse per se than any other type of data. However, it is useful to focus on sequence data here for several reasons. First, as the cost of sequencing has dropped, sequence data have become by far the least expensive data to gather for most studies. Second, analysis of sequence data allows one to study the molecular basis of evolution. Third, the analysis is somewhat more straightforward for molecular sequence data than for other types. The discrete and well-defined nature of the character traits (i.e., 4 nucleotides, 20 amino acids) makes quantifying trait evolution straightforward. Last, and most important, the principles that apply for molecular sequence data apply to other types of data as well.

The process of carrying out sequence-based phylogenetic analysis can be divided into four key steps (Fig. 27.1):

Select a sequence of interest. This could correspond to a whole gene, a region of a gene (coding or noncoding regions can be used), a regulatory region for a gene, a transposable element, or even a whole genome.

Identify homologs. Acquire sequence data for objects that are homologous to the sequence of interest

Align sequences. Align the sequence of interest and the homologous regions to generate a sequence data matrix.

Calculate phylogeny. Carry out phylogenetic inference on the alignment.

In this section, we discuss the first three steps. The last step&mdashphylogenetic inference&mdash is discussed in the section Methods Used to Infer Phylogenetic Trees.

Pattern analysis of phylogenetic trees could reveal connections between evolution, ecology

In biology, phylogenetic trees represent the evolutionary history and diversification of species -- the "family tree" of Life. Phylogenetic trees not only describe the evolution of a group of organisms but can also be constructed from the organisms within a particular environment or ecosystem, such as the human microbiome. In this way, they can describe how this ecosystem evolved and what its functional capabilities might be.

Now, researchers have presented a new analysis of the patterns generated by phylogenetic trees, suggesting that they reflect previously hypothesized connections between evolution and ecology. The study was led by Swanlund Professor of Physics Nigel Goldenfeld, who also leads the Biocomplexity Group at the Carl R. Woese Institute for Genomic Biology at the University of Illinois at Urbana-Champaign. The other members of the team were graduate student Chi Xue and former undergraduate student Zhiru Li, now at Stanford University. Their findings were published in a recent article in the journal Proceedings of the National Academy of Science, titled "Scale-invariant topology and bursty branching of evolutionary trees emerge from niche construction."

The most familiar phylogenetic tree of all life on Earth uses genes from the essential cellular ribosomal machinery to represent species. By comparing the differences between the molecular sequences of the same genes on different organisms, researchers can deduce which organisms were descended from others. This idea led to the mapping-out of the evolutionary history of life on Earth and the discovery of the third domain of life by Carl R. Woese and collaborators in 1977.

Real phylogenetic trees are complex branching structures, reflecting the pattern of speciation as new mutants emerge from a species. The branching structures are complex, but it is possible to characterize them in terms of how balanced they are and other statistical features reflecting the topology of the tree. The simplest characterization is to look at each branching node on the tree: does it split into two branches of exactly the same length or are the branches unequal in length? The former is said to be balanced while the latter unbalanced.

Despite the complexity of trees, there is a consistent mathematical pattern in topological structure across evolutionary time, one that is self-similar or fractal in nature. Using a minimal representation of evolution, the researchers showed how this fractal structure reflects the indelible imprint of the interplay between ecological and evolutionary processes. Minimal models of nature do not aim to be overly realistic but instead are constructed to capture the most important ingredients of a process in a way that makes simulation and mathematical analysis easy.

Goldenfeld's work frequently uses minimal models in order to explain generic aspects of complex biological and physical phenomena that are insensitive to precise details. Other aspects of complex phenomena cannot be described well in this way, but physical patterns such as self-similarity in space are known to be describable using minimal modeling approaches.

"Thus, it seemed reasonable to try this approach to describe self-similarity in time too" Goldenfeld said.

"We set off to study the topological property of the phylogenetic tree and ended up with an extra 'fruit of explanation" for the tree's special character,'" Xue said.

The study revolved around a concept in evolutionary ecology known as niche construction, first proposed about 40 years ago. In niche construction, organisms modify their environment, thereby creating new ecological niches in the ecosystem and changing the environment. In turn, these new niches affect the overall evolutionary trajectory of the organisms that share the environment. The end result is that evolution and the environment are coupled closely together. The idea that evolution is not occurring on a purely static environmental background is controversial, despite being intuitively appealing. Their findings add to the existing body of work by identifying the long term effects of niche construction in a way that can be detected by modern genomics and phylogenetic tree construction.

In the work reported here, researchers simulated organisms and associated to them a niche value that described their interaction with their environment. Those organisms with a large niche value contained a large number of ways to adapt to their environment and ultimately led to their survival while those with small niche values were less resilient.

"In our model, we relate the niche positively to the speciation probability, in the sense that an organism with a large niche can likely diversify successfully," Xue said. "During the phylogenetic tree evolution, when two daughter nodes emerge from their parent, they get their niches partially from inheriting and partially from construction."

Researchers showed that species which run out of niche space can no longer branch or speciate. Mathematically, this was represented as a so-called absorbing boundary condition on the node representing this species.

"Its sister node likely still diversifies as long as that niche is still positive, but the two sister nodes are no longer symmetric and the tree becomes unbalanced," Xue explained. "We demonstrated that the absorbing boundary is crucial to generate the fractal structure of the tree and that the niche construction guarantees that some nodes will reach the boundary."

The researchers used a simplified model of niche construction and were able to recapitulate the fractal scaling in the tree topology. Their calculations used methods adopted from a completely different field of science: the physics of phase transitions. An example of a phase transition is when a material such as iron becomes magnetic as its temperature is lowered. The magnetism emerges gradually once the temperature falls below a critical value.

Goldenfeld explained how this unusual analogy works: "Very close to this critical temperature, a magnet also is fractal or self-similar: it is structured into nested regions of magnetic and non-magnetic domains. This nesting or self-similar structure in space is reminiscent of the nesting or self-similar structure of bifurcating tree branches in time." Using computer simulations and the mathematics of phase transitions, the research team was able to demonstrate how the fractal scaling of the tree topology emerges.

"Our model has a small number of components and assumes simple mathematical form and yet, it generates the power-law scaling with the right exponent that is observed in actual biological data," Xue explained. "It's simply amazing to see how much a minimal model can do."

"We were able to reproduce not only the power-law behavior but also a non-trivial exponent that's very close to reality," Liu said. "In other words, the simulated trees are not only scale-invariant but also realistic in a way."

In addition to describing the fractal topology of phylogenetic trees, the model also accounted for the patterns of evolutionary clades previously documented to occur in microbial communities by Illinois Professor of Plant Biology James O'Dwyer, an ecologist trained in theoretical physics like Goldenfeld.

"It was especially gratifying to be able to gain some insight into James' earlier discovery, using a conceptual toolkit that came from statistical physics," Goldenfeld commented. "This work exemplifies the way in which powerful and unexpected results can arise from trans-disciplinary research, painstaking data analysis and minimal modeling."

The presence of niche construction creates a significant footprint in the evolutionary trajectory that cannot be eliminated, even across long time scales. The idea that niche construction -- which is based on a much shorter time scale -- emerges as a long-term memory in phylogenetic trees may surprise some people. Indeed, Liu adds that this "scale-interference" is also a hallmark of phase transitions, where the spacing between atoms in a magnetic crystal on the scale of Angstroms can influence the material properties on the scale of centimeters.

"When I learned about the idea of scale-interference in Nigel's physics class on phase transitions three years ago, I wasn't expecting any of the following: joining his group, applying this idea and solving a biological problem," said Liu. "Now I'm glad that I didn't doze off during that lecture."


For the first time, we have an integrative picture of the evolution of fin configurations and covariation patterns of these appendages among a large diversity of lower vertebrates. The two objectives of this paper were (1) to examine the morphological disparity in fin configurations among basal vertebrates and gain insight into the sequential appearance of median and paired fins in fishes, and (2) to investigate macroevolutionary patterns of co-occurrence among some of the fins, which could then be interpreted as evolutionary modules. These two objectives are not independent. The evolutionary emergence of novel fins could involve the duplication or co-option of pre-existing fin modules. Such scenarios have already been proposed, whether or not explicitly, in the context of the evolution of paired fins in early vertebrates [6, 41], the pectoral and pelvic fins in gnathostomes [17], the spine-brush-complex in symmoriiform sharks [110], the adipose fin in euteleosts [5, 103, 111], and the spinous dorsal fin in acanthomorphs [39]. Modularity also promotes functional and morphological disparity, because modules can be individually optimized without affecting other parts of an organism [22, 32, 112, 113]. Thus, a modular organization of appendages is useful to explain the disparity of fin configurations in fishes, but also at a larger scale of limbs in all vertebrates. The paired appendages of tetrapods provide a very telling example: the fore- and hindlimbs can be modified independently, which was a necessary prerequisite for the evolution of specialized structures, such as the wings in birds or bats [17, 46].

Disparity in fin configurations

The mapping of fin characters on the supertree reveals which groups are the most disparate in their fin configurations: agnathans, chondrichthyans, and derived actinopterygians display the greatest disparity in fin configurations, although they differ as to which fins are responsible for generating this disparity. Among agnathans, new fins are sequentially added and long ribbon-like fins are gradually modified into more spatially constricted median and paired fins. Thus, the disparity in this part of the tree seemingly results from tinkering with fin configurations and building towards the gnathostome Baüplan. In chondrichthyans, the most important source of disparity is the loss of some (occasionally all) of the median fins. The most disparate fin combinations are found among teleosteans, owing to frequent losses affecting median and/or paired fins, additions of novel fins, or duplications of pre-existing fins.

In agnathans, all of the fins (with the exception of the adipose and pelvic fins that are absent) participate in the observed patterns of disparity in fin configurations. Much of this disparity can be accounted for by the gradual modification of long-based median and paired finfolds into shorter-based dorsal, anal, and pectoral fins. By gradual modifications, we mean that it is seemingly a period where the morphospace is explored, resulting in various combinations of shorter- and longer-based median and paired fins. For instance, shorter-based paired fins appear to have evolved multiple times independently (e.g., Rhyncholepis and Kerreralepis among birkeniid anaspids Lanarkia, Phlebolepis, Turinia, and Shielia among thelodonts) before the emergence of true pectoral fins as can be found among osteostracans. Absence of the caudal fin also stands out as a source of disparity, yet this is restricted to a few species of hagfishes and lampreys. Among these, two extinct species, the putative hagfish Gilpichthys greenei and the putative lamprey Pipiscius zangerli, might in fact represent larval organisms [114, 115]. As such, the specimens assigned to these two taxa might not represent adult morphologies, and the scoring of characters could have differed in metamorphosed specimens. In extant species, the caudal fin is generally present, although it can be vestigial or even absent (e.g., Myxine formosana [116, 117]). As for the paired fins, ventrolateral paired fins are variably present among anaspids and thelodonts, while shorter-based paired fins that have a position reminiscent of gnathostome pectoral fins are found in some thelodonts and in the osteostracans.

The disparity in fin configurations that is apparent in the chondrichthyan part of the phylogeny can appear surprising given only the modern forms. Paleozoic chondrichthyans, however, present highly disparate morphologies, comparatively making modern holocephalans and elasmobranchs seem conservative [67, 118–121]. Most of the disparity in fin configurations for chondrichthyans can be accounted for by changes in the number of median fins that are present. The anal fin is lost in representatives of numerous chondrichthyan orders. In contrast, the dorsal fin is lacking only in a few chondrichthyan taxa. Most chondrichthyans have two dorsal fins, although the presence of a single dorsal fin is common. There is also some disparity due to the occasional loss of the caudal fin in some batoids. Batoids are characterized by dorso-ventrally flattened bodies, greatly enlarged pectoral fins, and in many species, a long whip-like tail. Propulsion in most of these forms is achieved through undulations (e.g., most skates and sting rays) or oscillations (e.g., eagle rays) of the widened pectoral fins [122–124], which provides a functional context for the loss of the caudal fin when compared to most other chondrichthyans that use a caudal fin-based propulsion. The paired fins do not account for much of the disparity in fin configurations: absence of the pelvic fins is limited to representatives of a single order of extinct chondrichthyans, the Eugeneodontiformes.

In derived actinopterygians, an important part of the disparity in fin configurations relates to the presence/absence of the pelvic fins and to the number of dorsal fins. Pectoral fins are lost far less frequently than the pelvic fins. For instance in teleosteans, the loss of pelvic fins has been reported in more than 100 families belonging to 20 different orders [125], whereas the loss of pectoral fins is reported for only eight teleostean orders in our dataset. The more frequent loss of the pelvic fins could reflect their lesser functional importance for swimming, when compared to the pectoral fins [125–128]. Although this study used a chondrichthyan model, experiments on fin amputations performed on the smooth dogfish (Mustelus canis) had shown that the sharks were able to correct for the loss of the pelvic fins using their median and pectoral fins [127]. In contrast, Standen [129] showed that in the rainbow trout (Oncorhynchus mykiss), the pelvic fins accomplished complex motions, indicating that their functional importance might have been underestimated. From an eco-morphological perspective, loss of the pelvic fins is often seen in fishes that possess an elongated body shape and occupy complex habitats such as coral reefs or crevices [125, 130, 131]. In these elongated fishes, the pectoral fins are often reduced as well, while the median fins are expanded in length and confluent with the caudal fin [131]. In tetrapods, limb reduction and body elongation are often associated with fossorial or semi-fossorial organisms [132–134]. Thus, in structure-rich habitats, the presence of paired lateral appendages could be disadvantageous, particularly for burrowers or parasitic fishes [135]. Additionally, some of these elongated fishes use anguilliform locomotion, which involves undulations along the entire body length and less emphasis on the use of the paired fins for propulsion [128, 136]. From a macroevolutionary perspective, another hypothesis to explain that the pelvic fins are more frequently lost than the pectoral fins is that pelvic fins appeared after the pectoral fins during the evolutionary history of fishes [11, 20], although an alternative hypothesis has been proposed whereby the pelvic fins appeared first among the anaspids [109]. Additionally, from a developmental perspective, pectoral fins develop prior to the pelvic fins [137, 138], and it has been observed that structures that develop last also tend to be the first to be lost through pedomorphosis [139]. For instance, in reptiles and lissamphibians, patterns of limb reduction reflect developmental sequences: the digits that develop last are the first to be lost in species with reduced limbs [105, 132].

The pelvic fins are frequently lost independently from the pectoral fins: this is observed in at least some representatives of two placoderm orders, one chondrichthyan order and 26 actinopterygian orders. The converse is rare, however. Among piscine gnathostomes, pectoral fin loss is restricted to actinopterygian taxa, and in seven of the eight orders where the pectoral fins are occasionally lost, the pelvic fins also tend to be absent. In fact, the loss of pectoral fins independently from the pelvic fins is only observed in some Stomiidae (Stomiiformes) and Pleuronectiformes. In stomiiform genera where this condition is observed, pectoral fins are present in larvae but are subsequently lost in juveniles and adults [140–145]. In Pleuronectiformes, some species lose their pectoral fins on a single side, while other species lose their pectoral fins on both sides as with Stomiiformes, this loss takes place during larval metamorphosis [146]. This suggests that loss of the pectoral and loss of the pelvic fins are not entirely independent, which would be an expectation for a paired fins evolutionary module.

The dorsal fin is also responsible for a large part of the disparity in fin configuration in derived actinopterygians: there can be one, two, or three separate dorsal fins, and it can also be entirely absent. There is usually a single anal fin, but it can also be lost, and there can occasionally be two anal fins. Similarly to the paired fins, there is evidence for non-independence in the dorsal/anal fin characters: in orders containing species with two anal fins, two or three dorsal fins tend to be present. Another source of disparity in median fin configurations is the adipose fin which is present in many derived actinopterygians. None of the ostariophysan or euteleostan species that have an adipose fin have second (or third) dorsal fins: instead, they generally have a single centrally placed dorsal fin and a posteriorly located anal fin [147]. Conversely, groups that are close relatives but lack an adipose fin tend to have a “fast-start” morphology with posteriorly placed dorsal and anal fins [147, 148].

Evolutionary history of fish appendages

Median fins

Median fins are present even in the earliest vertebrates. The most basal agnathan fishes are equipped with fairly well-developed median fins which include, in most cases, a caudal fin and elongated dorsal and ventral fins. For instance, the median ventral finfolds of myllokunmingiids span almost the full length of their bodies, as do their long sail-like dorsal fins [7–9, 149]. Myxiniformes also often possess long median ventral finfolds, which although sometimes interrupted around the cloaca, are continuous with the caudal fin. These elongated median fins are reminiscent of the median larval finfold observed during the early ontogeny of more advanced fishes [150, 151]. They are also reminiscent of the extensive dorsal and ventral finfolds found in the more basal cephalochordates, which are continuous around the tail, but also around the anterior tip of the notochord [152–154]. The median fins of cephalochordates are further described as being continuous with one of the two paired metapleural folds, but the latter can hardly be considered as fins because they are hollow structures filled with fluid [155, 156].

Even the most basal agnathans have a caudal fin. A caudal fin is absent, however, in Gilpichthys greenei and Pipiscius zangerli, two Carboniferous fossil fishes. Although these two taxa display clearly chordate characters, their assignment respectively to the Myxiniformes and Petromyzontiformes remains tentative, and both have been interpreted as possible larval organisms [115]. Thus, the absence of a caudal fin could reflect a larval condition. It is also possible that the apparent lack of a caudal fin is merely a taphonomic artifact. This could arguably be the case for Pipiscius, which presents a very posteriorly positioned dorsal fin that could certainly be interpreted as a dorsal extension of the caudal fin. Furthermore, only ten specimens were used for the original description [115]. This explanation is however less likely for Gilpichthys, its original description being based on more than 100 specimens [115]. Additionally, traces of the eyes, otic capsules, branchial pouches, and gut have been identified in both species, and these structures were shown to be less decay-resistant than the caudal fin [157, 158].

In more advanced agnathans, a long-based preanal finfold is generally absent. Instead, many taxa possess a shorter-based and more posteriorly positioned anal fin. An anal fin is present in all anaspids that are sufficiently known from their postcranial anatomy. Furthermore, a preanal fin and an anal fin never co-occur in agnathans, with the possible exception of two birkeniid anaspids for which a few spines and an anal plate located anteriorly to the anus [159–161] were provisionally interpreted as evidence for a median ventral fin. Most modern hagfishes and lampreys lack an anal fin. However, the presence of a true anal fin has been observed in a few specimens of Petromyzon marinus [162, 163] and of Lampetra planeri [164], a phenomenon that has been interpreted as a possible atavism [165, 166]. Anal fins have also been described in two Carboniferous lampreys, Hardistiella montanensis [167] and Mayomyzon pieckoensis [168]. Based on this evidence, Forey [169] suggested that the absence of an anal fin could be a synapomorphy of recent lampreys. Additionally, the Late Carboniferous hagfish Myxinikela siroka is described as having dorsal and ventral fins (= anal fin?) that are continuous with the caudal fin, as in Mayomyzon, although in his original description, Bardack [170] raised the possibility that Myxinikela might be a juvenile. Myxinikela, Hardistiella, and Mayomyzon represent some of the oldest Myxiniformes and Petromyzontiformes for which complete non-larval specimens are known and, combined with the atavistic reappearance of an anal fin in P. marinus and L. planeri, this suggests that the appearance of an anal fin occurred before the anaspids. Thus, an anal fin could be a plesiomorphic characteristic of vertebrates or even of craniates if the ventral fin of Myxinikela is homologous to an anal fin. An anal fin is absent in the oldest fossil lamprey, Priscomyzon, but phylogenetic analyses resolve Mayomyzon as the most basal petromyzontid, while Priscomyzon is more derived [171–173]. As for more crownward taxa, the presence of an anal fin is considered primitive for chondrichthyans, acanthodians, and osteichthyans its absence in some Paleozoic sharks (e.g., Cladoselache, stethacanthids, and symmoriids) is considered as a derived condition [174].

As opposed to the median ventral fin, the long-based dorsal fins of myllokunmingiids are not so rapidly modified into shorter-based dorsal fins. Many agnathan taxa bear short-based and comparatively more posteriorly positioned dorsal fins (Petromyzontiformes, Loganelliiformes, Shieliiformes, Phlebolepidiformes, Furcacaudiformes, Osteostraci), whereas the Jamoytiiformes retain elongated dorsal fins. Long-based dorsal fins also occur in numerous chondrichthyan (e.g., Pleuracanthus gaudryi, Chondrenchelys problematica) and osteichthyan (e.g., Regalescus glesne, Acanthurus major) taxa. It is reasonable to assume that the dorsal fin is not constrained in its anterior extent and position, as opposed to the anal fin, which cannot extend anteriorly past the position of the anus. The Gymnotiformes provide a striking example: these fishes have elongated anal fins that extend along the majority of the ventral midline of the body, yet the anus is displaced anteriorly in these forms, positioned under the pectoral fins or even under the head, thus remaining in front of the anterior limit of the anal fin [175–177].

Duplications of the dorsal fins

Duplications of the dorsal fin seem to have occurred numerous times independently during the evolutionary history of fishes. Most extant lampreys have two dorsal fins. Among osteostracans, Ateleaspis, Aceraspis, and Hirella possess two dorsal fins and are resolved as basal members of this group [15, 178–181]. Among the most basal orders of placoderms, antiarchs and stensioellids generally possess a single dorsal fin, but the material for brindabellaspids and pseudopetalichthyids precludes interpretation of dorsal fin characters. In other groups of placoderms where dorsal fin characters are known, ptyctodontids have two dorsal fins, whereas rhenanids and arthrodires have a single dorsal fin. Among acanthodians, climatiiforms, diplacanthiforms, and ischnacanthiforms have two dorsal fins. Acanthodiforms possess a single dorsal fin, but this is considered as secondarily derived for this group.

Lund [174] expressed that the plesiomorphic condition for the number of dorsal fins in chondrichthyans could not be determined at the time and could just as well have been a single dorsal fin or two dorsal fins. The most basal articulated undisputed elasmobranchs known from the fossil record, Doliodus problematicus and Antarctilamna prisca, have anterior dorsal fins, but most of the postcranial region is unknown and thus insufficient to assess the presence of a posterior dorsal fin [182, 183]. Additionally, in the Antarctilamna material, a spine with a shallow insertion that had initially been interpreted as a displaced dorsal fin spine is now thought to be a pectoral fin spine, whereas a second type of spine with a deeper insertion is interpreted as a median fin [109, 183, 184]. Furthermore, phylogenies have not reached a stable consensus concerning the interrelationships of basal Euchondrocephali (see, e.g., [185–187]). Our supertree analysis places the iniopterygians as the most basal euchondrocephalan order, although they are resolved as the sister clade to all other chondrichthyans in Lund et al. [186]. Of course, in light of the growing support for the hypothesis that acanthodians are stem chondrichthyans, this would imply that the plesiomorphic condition for the total group chondrichthyans is in fact the presence of two dorsal fins.

Among osteichthyans, the presence of two dorsal fins has been considered as plesiomorphic [188]. Guiyu oneiros, resolved as a stem sarcopterygian [60], was originally reconstructed with a single dorsal fin [189], but has recently been reinterpreted as having two dorsal fins [190]. All other sarcopterygians have two dorsal fins, with the exception of a few dipnoans, elpistostegalians, and tetrapods. The Early Devonian Dialipina is resolved either as a basal osteichthyan [54, 55, 58, 59, 61, 191–193] or as the most basal actinopterygian [57, 99, 102, 189, 194–197], and it possesses two dorsal fins [99]. Among other non-acanthomorph actinopterygians, a second dorsal fin is also found in a single fossil Ionoscopiformes species [100] and in a few extant Siluriformes belonging to the Plotosidae [1, 198–200]. This suggests that the presence of two dorsal fins would have been lost early during actinopterygian evolution [102], but that this character would have subsequently been reacquired more than once independently.

Acanthomorphs are characterized by the possession of an anterior spinous dorsal fin [201]. In some taxa the spinous and soft dorsal fins are continuous and connected by a fin web, whereas in others they are widely separated. In our scoring of characters, we considered that dorsal fins where the bases were not connected by a fin web constituted separate dorsal fins. The dorsal fin(s) of acanthomorphs can be interpreted in two different ways. One hypothesis is that the acanthopterygian anterior spinous dorsal fin results from a duplication of the posterior soft dorsal fin module [39]. Another hypothesis is that the second or third dorsal fin in acanthopterygians results from the subdivision of an originally more elongated fin [202]. As such, acanthomorphs retain a single dorsal fin which is regionalized, thus giving the impression that there are two (or three) dorsal fins [16]. Our supertree analysis places the Lampridiformes at the base of the acanthomorph radiation. The Aipichthyoidea, resolved as stem Lampridiformes [203, 204], possess a single dorsal fin, for which the anterior portion is generally supported by two to five fin spines [204–207], although there are 12 fin spines in Homalopagus multispinosus [207]. In crown Lampridiformes, dorsal fin spines are present in Veliferidae but are considered to have been secondarily lost in other forms [203]. Among other acanthomorph orders that were resolved as the most basal in our supertree analysis, Percopsiformes and Polymixiiformes also possess a single dorsal fin where the leading edge is generally supported by a few spines [1]. In light of this evidence, the hypothesis of a regionalized dorsal fin cannot be ignored.

Taken together, the phylogenetic distribution of dorsal fin conditions suggests that duplications of the dorsal fin occurred multiple times during the evolutionary history of fishes. It also suggests that two dorsal fins might have been the condition for the common ancestor to both osteostracans and gnathostomes. This character would have subsequently been lost and then occasionally reacquired in many fish lineages.

Paired fins

The first evidence of true paired fins in craniates is in the Anaspidiformes and Jamoytiiformes, generally in the form of long ribbon-like paired folds that are ventrolateral in position. A notable exception can be found in the Myxiniformes, where for a single genus, Neomyxine, we tentatively scored for the presence of ventrolateral paired fins. Neomyxine possesses paired folds of skin located immediately above the gill openings [208–210]. These skin folds are not used for swimming but rather as support when specimens settle on the substrate [209]. Furthermore, because these structures are located dorsally to the branchial apertures and because Neomyxine is not basal relative to other hagfishes, these paired skin folds are unlikely to be homologous to the ventrolateral paired fins found in other agnathans [49, 211], although some thelodonts also have paired fins that are inserted dorsally to the branchial apertures [63]. Thus, excluding Neomyxine, ventrolateral paired fins appear with the anaspids and can also be found in some thelodonts. The question regarding the homology of these paired fins has been debated for many years. Some authors consider that true paired fins must be constricted and supported by an endoskeletal girdle and fin radials [47, 48]. An alternative hypothesis is that paired fins evolved first as lateral extensions of the body, and that paired girdles only appeared later during the evolutionary history of basal vertebrates [109, 212]. Shubin et al. [17] proposed an evolutionary scenario whereby (1) paired fins first appeared as elongated ventrolateral expansions along the body wall, (2) these expansions were then modified into shorter-based pectoral appendages only, (3) and later pelvic fins appeared among gnathostomes as serial homologues of the pectoral fins. We find the latter hypothesis reasonable: it would not be surprising that paired and unpaired fins share a similar evolutionary history (Fig. 4) considering the remarkable anatomical and developmental similarities between the paired and unpaired fins [41, 151, 213]. Furthermore, based on gene expression patterns during fin development in lampreys and sharks, it was suggested that the genetic programming associated with median fin development was subsequently redeployed to the lateral mesodermal plate, giving rise to the paired fins [6, 41]. A previous study focusing on gene expression patterns in cephalochordates had similarly led Schubert et al. [214] to hypothesize that part of the developmental programs involved in tail outgrowth in basal chordates could have been co-opted towards paired appendage development in vertebrates. Alternatively, it could be argued that the pelvic fins, and not the pectoral fins appeared first [109], or that paired fins evolved multiple times independently during the evolutionary history of vertebrates [215].

Hypothesized scenario for the evolution of median and paired fins. Both median and paired fins developed first as elongated ribbon-like structures (a) that are gradually modified into short-based fins (b). Serial duplications of fin modules lead to the emergence of novel fins such as the pelvic fins or a second dorsal fin (c). Divergence or co-option of some fin modules also leads to the evolution of novel fins, such as the adipose fin of euteleosts or the spinous dorsal fin of acanthomorphs (d)

As for short-based paired fins, true pectoral fins are considered to have appeared with the osteostracans, although pituriaspids also have pectoral fenestrae, suggesting that pectoral fins were present in these taxa as well [216]. The pectoral fins of osteostracans are supported by endoskeletal elements and are under muscular control: they can thus be considered as homologous to the pectoral fins of gnathostomes [11, 13, 15]. Additionally, some thelodonts possess muscularized and moveable paired fins that are in a pectoral position [11, 63, 217]. Girdle-supported pelvic fins are absent in agnathans [18, 47, 190, 211] and are first observed among placoderms [16, 18, 19]. Antiarch placoderms have been resolved at the base of the gnathostome diversification in most of the recent phylogenetic studies [54–57, 59, 61] and were thought to be devoid of pelvic fins [65]. However, Zhu et al. [18] recently described a pelvic girdle in Parayunnanolepis. Additionally, our supertree analysis places the Pseudopetalichthyida stemward to the antiarch placoderms, making it the most basal gnathostome order. The most well-preserved pseudopetalichthyid articulated material belongs to Pseudopetalichthys problematica, which is known to possess both pectoral and pelvic fins [218]. This suggests that the presence of pelvic fins is likely to be plesiomorphic for gnathostomes.

Evidence for fin evolutionary modules

Based on the mapping of fin characters on the supertree, some pairs of fins are more frequently associated, either through coordinated duplication events or through coordinated losses, which is congruent with hypotheses that together they form evolutionary modules. This is the case for the dorsal and anal fins where the presence of a second anal fin is associated with the presence of a second or third dorsal fin. Mabee et al. [39] suggested that the dorsal and anal fins were linked through the presence of both positioning and patterning modules. Although patterning modules refer to the development of endo- and exoskeletal supports [39, 40, 219], the effect of the patterning module could extend to the resorption of the larval median finfold. More precisely, during fish larval development, there are generally dorsal and ventral median finfolds that are continuous with a caudal finfold [150, 151]. During development, these finfolds are resorbed except in places where dorsal, anal, and caudal fins will develop [151]. Here, we hypothesize that the mechanism underlying duplication of a non-resorption zone of the larval finfold could very well be reflected dorso-ventrally, leading to coordinated duplications of the dorsal and anal fins. This pattern also emerges in their coordinated loss patterns. For instance, in actinopterygians, results from the multiple correspondence analyses suggest that loss of the dorsal, anal, and caudal fins can be coordinated. Likewise, the results also show that loss of the pectoral and pelvic fins can be coordinated. Coordination of fin losses is not limited to actinopterygians: the results of the multiple correspondence analyses for chondrichthyans and sarcopterygians also show coordinated losses of the median fins. Evidence for a dorsal and anal fins evolutionary module has been proposed for lungfish, in light of the observations that, in earlier forms, the dorsal and anal fins present equivalent positions along the antero-posterior body axis, that they have similar morphologies, particularly with respect to fin supports, and that they were coordinately lost at the end of the Devonian [220]. It is unclear, however, if the dorsal and anal fins module suggested in Johanson et al. [220] involves the anterior dorsal fin, the posterior dorsal fin, or both dorsal fins. At a population scale, it was found that in the Arctic charr (Salvelinus alpinus), anatomical and developmental patterning of the dorsal and anal fins were highly similar, but differed largely from that of the caudal fin: this was interpreted as supporting the patterning modules proposed by Mabee et al. [39] for the dorsal and anal fins [219, 221]. A patterning module was also hypothesized for the caudal fin [219]. In contrast, in a recent study focusing on variational modularity in two cyprinid species, we showed good support for the hypothesis that the dorsal, anal, and caudal fins formed one variational module including the caudal peduncle, while the paired fins formed another variational module [222]. Because modularity is a hierarchical concept, a hypothesis of evolutionary modularity worth investigating is that the median fin system as a whole could constitute one module, the paired fin system could constitute a second independent module, and the dorsal and anal fins could constitute a third module nested within the median fins module (Fig. 5). Quasi-independent median and paired fin modules would help explain why there is so much disparity in median fin configurations in chondrichthyans, compared to the paired fins, which are largely unaffected.

Hypothesized fin modules. The pectoral and pelvic fins form a paired fins evolutionary module that can be dissociated, leading to individualized pectoral and pelvic fin modules. The dorsal and anal fins form a second evolutionary fin module nested within a larger median fins evolutionary module

We have demonstrated that the co-occurrence of some sets of fins is non-random. Among these, the pectoral, pelvic, dorsal, anal, and caudal fins have all been found to be non-independent. This reflects the most common fin combinations found in the dataset where all of these fins co-occur, more specifically, the fin combinations that are characteristic of most actinopterygian orders (single dorsal and anal fins, a caudal fin, pectoral and pelvic fins) and of most chondrichthyan and sarcopterygian orders (two dorsal fins, a single anal fin, a caudal fin, pectoral and pelvic fins). When the analysis focuses on unique fin combinations, only the pectoral/pelvic fins show non-independence. The strong relationship between the pectoral and pelvic fins is concurrent with hypotheses that they form a paired fins evolutionary module.

A relationship was also found between the adipose fin and the median ventral fin. The adipose fin is considered as an evolutionary novelty among teleostean taxa and might also constitute a new fin module [103, 110]. An adipose fin evolved at least twice independently, once within the Otophysi and a second time in the Euteleostei [5, 103]. Development of the adipose fin is known to differ between otophysans and euteleosteans, supporting the hypothesis of multiple independent origins: in Characiformes, the adipose fin appears as an outgrowth following the complete resorption of the larval finfold, while in Salmoniformes, it develops as a remnant of the larval finfold [5]. As for the median ventral fin, the positive relationship with the adipose fin stems from a few euteleostean families that, in addition to the adipose fin, possess a rayless finfold in front of the anal fin that is often described as a ventral adipose fin (Retropinnidae, Stomiidae, Paralepididae). However, a similar ventral fin is also found in at least one family, the Sundasalangidae (Clupeiformes), prior to the appearance of the adipose fin, as well as in euteleostean families that do not have adipose fins (Phallostethidae, Hypoptychidae). As opposed to the adipose fin which has been the object of numerous recent investigations [5, 103, 111, 147, 148], to our knowledge no work has focused on the origin or homology of the so-called ventral adipose fin. Developmental and histological work would be necessary to establish if this median ventral fin is homologous among these taxa.

A dorsal-anal fin module is well supported by developmental data [40–42, 219, 221, 223]. It has also been inferred based on the similarities in the relative positioning of these two fins across species [39]. Because the positioning module inferred by Mabee et al. [39] has been identified at a macroevolutionary scale, it qualifies as an evolutionary module. Herein, we provide further evidence for a dorsal-anal fin evolutionary module, with indications that its effect also extends to the coordinated losses and duplications of these fins in different species.

Co-occurrence of the pectoral and pelvic fins is extremely well supported in our analyses. Both paleontological and embryological studies support the idea that the pelvic fins could have originated by a duplication of the pectoral fins module [20, 21, 224, 225]. Based on this hypothesis, it follows that the co-occurrence of these two fins would be expected. An alternative possibility is that the pectoral and pelvic fin modules have dissociated and become independent modules during the evolutionary history of fishes [10, 20, 45, 46, 226]. As evidence for this latter hypothesis, Coates and Cohn [10] mentioned that there is no example in which the pelvic appendages are a direct copy or identical serial homologues of the pectoral fins. Additionally, some primitive gnathostomes (e.g., Parayunnanolepis, Kathemacanthus, Lupopsyrus, Brochoadmones, Cheirolepis) have pectoral and pelvic fins that are both anatomically different and positionally decoupled [109]. One could argue, however, that the paired fins present extremely similar morphologies in chimaerids (C. Riley and E. Grogan, personal communication R. Cloutier, personal observation) and in many sarcopterygians [188, 190]. Furthermore, biserial fin designs evolved convergently in pectoral and pelvic fins in some chondrichthyan and sarcopterygian taxa, as did uniserial fin designs in osteolepiforms [105]. Considering that independent loss of the pectoral or pelvic fins occurs almost only in actinopterygians, perhaps the dissociation of the paired fins module is a generalized characteristic for this group, which was independently acquired in eugeneodontiform sharks.

Comparative and phylogenetic perspectives of the cleavage process in tailed amphibians

The order Caudata includes about 660 species and displays a variety of important developmental traits such as cleavage pattern and egg size. However, the cleavage process of tailed amphibians has never been analyzed within a phylogenetic framework. We use published data on the embryos of 36 species concerning the character of the third cleavage furrow (latitudinal, longitudinal or variable) and the magnitude of synchronous cleavage period (up to 3–4 synchronous cell divisions in the animal hemisphere or a considerably longer series of synchronous divisions followed by midblastula transition). Several species from basal caudate families Cryptobranchidae ( Andrias davidianus and Cryptobranchus alleganiensis ) and Hynobiidae ( Onychodactylus japonicus ) as well as several representatives from derived families Plethodontidae ( Desmognathus fuscus and Ensatina eschscholtzii ) and Proteidae ( Necturus maculosus ) are characterized by longitudinal furrows of the third cleavage and the loss of synchrony as early as the 8-cell stage. By contrast, many representatives of derived families Ambystomatidae and Salamandridae have latitudinal furrows of the third cleavage and extensive period of synchronous divisions. Our analysis of these ontogenetic characters mapped onto a phylogenetic tree shows that the cleavage pattern of large, yolky eggs with short series of synchronous divisions is an ancestral trait for the tailed amphibians, while the data on the orientation of third cleavage furrows seem to be ambiguous with respect to phylogeny. Nevertheless, the midblastula transition, which is characteristic of the model species Ambystoma mexicanum (Caudata) and Xenopus laevis (Anura), might have evolved convergently in these two amphibian orders.

2.4: Perspectives on the Phylogenetic Tree - Biology

How to Draw a Phylogenetic Tree
(Using differences in molecular sequence)

A phylogenetic tree uses data to indicate relatedness of different species. This webpage explains how to construct a phylogenetic tree using differences in molecular sequences (such as differences in amino acids, or differences in nucleotides).

Numbers in the table below represent mutational differences in a particular gene. Higher numbers indicate more genetic differences between two species. The longer two species (or subspecies) are isolated, the more likely there will be an accumulation of mutational differences.

1. Identify the most different, or ancestral, species . This is the one that has the most mutational differences from the other species. In the chart above, the species with the most mutational differences (highest numbers) is Species A .

2. Select the next most different, or ancestral species, the one that shares a common ancestor with the previous species ( Species A ). To do this, look at the Species A column and look for the species that has the fewest mutational differences, which is Species B with 27.

3. Begin drawing the phylogenetic tree. This is commonly done by drawing a line with branches indicating a possible shared common ancestor. The break (or node) of a branch indicates a common ancestor, and the branch itself indicates speciation. In a phylogenetic tree, line length does not necessarily indicate the age of a species, just relatedness and ancestry.

4. Add the next organism . To do this, look at the second organism's data ( Species B ), and look for the most genetically similar organism (for that particular gene). From the table, Species B may share a common ancestor with Species C (13 differences).

5. Add the next organism. Looking at the Species C row and column, find the most genetically similar organism, which is Species D (3 differences).

6. Add the remaining organisms. Looking at Species D , the lowest number is still the "3" from the mutation differences with Species C . What this may indicate is that Species D shares a common ancestor with Species C , but not with the remaining species ( Species E and Species F ). Looking at Species E and Species F data, Species E is very similar to Species F , and Species E is similar to Species C . This suggests that Species E shared a common ancestor with Species C , not Species D . Species F then shares a common ancestor with Species E .

7. Check to confirm that your phylogenetic tree matches the data in the table.

2.4: Perspectives on the Phylogenetic Tree - Biology

Reading trees: A quick review

A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms, called taxa (singular: taxon). The tips of the tree represent groups of descendent taxa (often species) and the nodes on the tree represent the common ancestors of those descendants. Two descendents that split from the same node are called sister groups. In the tree below, species A & B are sister groups — they are each other's closest relatives.

Many phylogenies also include an outgroup — a taxon outside the group of interest. All the members of the group of interest are more closely related to each other than they are to the outgroup. Hence, the outgroup stems from the base of the tree. An outgroup can give you a sense of where on the bigger tree of life the main group of organisms falls. It is also useful when constructing evolutionary trees.

For general purposes, not much. This site, along with many biologists, use these terms interchangeably — all of them essentially mean a tree structure that represents the evolutionary relationships within a group of organisms. The context in which the term is used will tell you more details about the representation (e.g., whether the tree's branch lengths represent nothing at all, genetic differences, or time whether the phylogeny represents a reconstructed hypothesis about the history or the organisms or an actual record of that history etc.) However, some biologists do use these words in more specific ways. To some biologists, use of the term "cladogram" emphasizes that the diagram represents a hypothesis about the actual evolutionary history of a group, while "phylogenies" represent true evolutionary history. To other biologists, "cladogram" suggests that the lengths of the branches in the diagram are arbitrary, while in a "phylogeny," the branch lengths indicate the amount of character change. The words "phylogram" and "dendrogram" are also sometimes used to mean the same sort of thing with slight variations. These vocabulary differences are subtle and are not consistently used within the biological community. For our purposes here, the important things to remember are that organisms are related and that we can represent those relationships (and our hypotheses about them) with tree structures.

Evolutionary trees depict clades. A clade is a group of organisms that includes an ancestor and all descendants of that ancestor. You can think of a clade as a branch on the tree of life. Some examples of clades are shown on the tree below.

2.4: Perspectives on the Phylogenetic Tree - Biology

Using trees for classification

    One has a longer history than the other. The first representatives of the cat family Felidae probably lived about 30 million years ago, while the first orchids may have lived more than 100 million years ago.

Orchids of these two different genera hybridize. . but cats of these two different genera do not.
Laelia Cattleya Felis Panthera

There is just no reason to think that any two identically ranked groups are comparable and by suggesting that they are, the Linnaean system is misleading. So it seems that there are many good reasons to switch to phylogenetic classification. However, organisms have been named using the Linnaean system for many hundreds of years. How are biologists making the transition to phylogenetic classification?

Switching to phylogenetic classification

Biologists deal with phylogenetic classification by de-emphasizing ranks and by reassigning names so that they are only applied to clades. This means that your use of biological names doesn't have to change very much. In many cases, the Linnaean names are perfectly good in the phylogenetic system. For example, Aves, which is the class of birds in the Linnaean system, is also used as a phylogenetic name, since birds form a clade (right).


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