Saturday, September 15, 2012

Snapshots of Old Fish Phylogenies, Part I


Phylogenetics became a science with a consistent and objective methodology after the introduction of phylogenetic systematics, or cladistics, by Willi Hennig in the 1950s and 1960s (1, 2). As a life-long student of ichthyology and a scientist who specializes in phylogenetic methods, I have been interested in hypotheses and graphical depictions of phylogenetic relationships of ray-finned fishes that were published prior to the introduction of cladistics.

There is no longer much attention paid to these early views of fish phylogeny, which I think is unfortunate. There is an opinion that with the advent of cladistics, there is no need to study and understand these pre-cladistic hypotheses of fish relationships. However, it is important to note that most biologists in the 19th Century immediately accepted Darwin’s fundamental thesis that all life on Earth shares common ancestry (3). Notable examples of ichthyologists that never accepted evolution include Louis Agassiz, a professor at Harvard University, and Albert K. L. G. Günther. The late 19th and early 20th Century ichthyologists that were thinking about how lineages of fishes were related to one another were explicitly attempting to create taxonomies that reflect hypothesized genealogical relationships. The problem is that prior to Hennig there was no standard method to infer these relationships, which meant that even when using the same type of information scientists could arrive at dramatically different conclusions about phylogeny.

Phylogeny of teleost fishes from E.D. Cope's book, Primary Factors of
Organic Evolution, 1896.
After starting to offer an ichthyology course at the University of Tennessee, and now at Yale University, I started to become interested in the history of the scientific study of fish phylogeny to augment and accentuate my lectures. My foray into pre-cladistic fish phylogenies was greatly helped by Colin Patterson’s masterly review that successfully demonstrates the influence fossil lineages had on the study of teleost relationships (4), with Patterson’s thesis that the most direct path to the inference of phylogeny is the study of living lineages (5).

It is not entirely clear to me what we can specifically learn by studying pre-cladistic efforts at fish phylogeny. Will we discover a hypothesis that is now again finding support in explicit post-Hennig phylogenetic analyses, or will we see reflections of both method and theory that will allow a more nuanced view of how we approach phylogeny inference in the 21st Century? Even if there are no obvious undiscovered gems in these old phylogenetic trees, an understanding of this history will minimally allow us to appreciate the set of objective approaches shared by most comparative biologists interested in phylogeny, regardless of the group of organisms investigated. What I think we do see in these old trees is that the approach used by different scientists to infer relationships was idiosyncratic and often limited by the patterns of biological diversity exhibited in the specific organismal lineage.

Phylogeny of fishes from Gill's 1871 work,
Arrangement of the Families of Fishes, or
Classes Pisces, Marsipobranchii, and
Leptocardii
Among the earliest diagrammatic fish phylogenies are from 1866 (6) by Ernst Haeckel (1834-1919), who is credited with the introduction of the term “phylogeny.” One of the first comprehensive post-Darwin classifications of fishes was introduced by Edward D. Cope (7-9). Cope emphasized osteology as evidence for his conclusions on relationships of fishes (8, p. 446). Cope’s publications on ray-finned fish classification did not include any diagrammatic representation of phylogeny, but his work is noteworthy for the description of Actinopteri and the delimitation of Nematognathi that includes catfishes and sturgeons, and the decision to not recognize Müller’s Teleostei. Twenty-five years later Cope published a branching diagram that represented his views on relationships of what would encompass the teleosts in his book “Primary Factors of Organic Evolution (10).”

The earliest fish phylogeny shown here is from Theodore Gill’s very influential and informed classification of fishes that includes Cope’s Nematognathi and Müller’s Teleostei (11, p. xliii), which as mentioned above, was not recognized by Cope.

Phylogeny of ray-finned fishes from Dean's book
Fishes, Living and Fossil, 1895.
The next fish phylogeny shown here is from Bashford Dean’s (1867-1928) book “Fishes, living and fossil” published in 1895 (12). Dean does not discuss any specifics of this tree, but it appears to reflect Cope's classification because it shows a close relationship of catfish and sturgeons (Nematognathi). Dean was impressed with teleosts stating, “Teleosts have diverged most widely of all fishes from what seem to have been their primitive structural conditions.” Later, Dean notes that convergent evolution is pervasive among teleosts and this makes inferences regarding relationships within the group difficult, “Environment, like a mould, has impressed itself upon forms genetically remote, and in the end has place them side by side, apparently closely akin, similar in form and structure (12, p. 167).”

Part II will begin with George A. Boulenger.

References

1.  Hennig, W. 1950. Grundzüge einer Theorie der phylogenetischen Systematik. Berlin: Deutscher Zentralverlag.
2.  Hennig, W. 1966. Phylogenetic systematics. Urbana: University of Illinois Press.
3.  Darwin, C. 1859. On the origin of species. London: John Murray.
4.  Patterson, C. 1977. The contribution of paleontology to teleostean phylogeny, in Major patterns in vertebrate evolution, P.C. Hecht, P.C. Goody, and B.M. Hecht, Editors. Plenum Press: New York. p. 579-643.
5.  Patterson, C. 1981. Significance of fossils in determining evolutionary relationships. Annual Review of Ecology and Systematics. 12:195-223.
6.  Haeckel, E. 1866. Generalle morphologie der organismen. Berlin: G. Reimer.
7.  Cope, E.D. 1871. Observations on the systematic relations of the fishes. American Naturalist. 5:579-593.
8.  Cope, E.D. 1871. Contribution to the ichthyology of the Lesser Antilles. Transactions of the American Philosophical Society. N.S., 14:445-483.
9.  Cope, E.D. 1872. Observations on the systematic relations of the fishes. Proceedings of the American Society for the Advancement of Science. 20:317-343.
10.  Cope, E.D. 1896. Primary factors of organic evolution. Chicago: The Open Court Publishing Company.
11.  Gill, T.N. 1872. Arrangement of the families of fishes, or classes Pisces, Marsipobranchii, and Leptocardii. Smithsonian Miscellaneous Collections. 11:i-xlvi, 1-49.
12.  Dean, B. 1895. Fishes, living and fossil. New York: Columbia University Press.

Friday, September 14, 2012

Nuclear Genes Result in a Resolved Squirrelfish-Soldierfish Species Tree


Fifteen years ago Wayne Maddison articulated a vision for phylogenetics, which was realized with the introduction of methods that incorporate coalescent theory into molecular phylogenetic inferences (1, 2). These “species tree” methods attempt to estimate the optimal tree that contains the set of sampled gene trees, using simple coalescent models to account for ancestral polymorphism (3).

There is a growing frequency of fish phylogenetic studies that are using multi-locus DNA sequence datasets analyzed with species tree methods (e.g., 4). Most molecular phylogenetic studies of closely related animals have relied on mitochondrial DNA because there is no recombination in the mitochondrial genome and the rate of nucleotide substitution is substantially higher than nuclear DNA. Also, universal primers to amplify specific regions of the mtDNA genome have been around since the late 1980s (5). This historical reliance on mtDNA means that we do not really know if we can expect phylogenetic resolution for clades of closely related species when sampling DNA sequences from a modest number of nuclear genes.

A print of Holocentrus ascensionis sampled
from Wikipedia
My graduate student Alex Dornburg is working on the phylogenetic relationships and patterns of diversification in the teleost clade Beryciformes. The first paper from his work on these fishes was published this week in MPE (6). Alex’s paper focuses on the phylogenetic relationships of the beryciform lineage Holocentridae (Squirrelfishes and Soldierfishes), a clade of 84 large eyed and primarily nocturnal species. The most recent common ancestor of living holocentrid species is minimally dated at 50 million years ago based on the phylogenetic relationships of two fossil holocentrid species from the Pesciara beds at Bolca, Italy (7-10). The Eocene age of the clade indicates that many holocentrid species likely share a fairly recent common ancestry.

Alex worked with a closely with a Yale College student, Rachel Webster, to compile a nice dataset of DNA sequences of six protein coding genes sampled from 39 holocentrid species. A single mtDNA gene was sequenced as well because data for this gene was available on Genbank for Corniger spinosus, which we did not have access to specimens for DNA sequencing. The phylogenetic analyses of the concatenated nuclear genes, as well as the species tree inference, were well resolved with very impressive bootstrap and Bayesian posterior clade support. We included the mtDNA gene and the 6 nuclear genes in a subsequent set of phylogenetic analyses, including a species tree inference. Inclusion of the mtDNA tree did not appear to alter the phylogenetic inferences, nor did it increase the posterior clade support in the *BEAST inferred species tree. These results indicate that DNA sequences sampled from a set of nuclear genes result in a strong inference of phylogenetic relationships among the closely related species of Holocentridae.
Phylogenetic relationships of Holocentridae inferred from six nuclear genes. A. Optimal tree from RAxML anlaysis, black and open circles are strong bootstrap values. B. Maximum clade credibility tree from a MrBayes analysis, black and open circles denote nodes with a Bayesian posterior equal to or greater than 0.95. C. *BEAST inferred maximum clade credibility species tree, black and open circles denote nodes with a Bayesian posterior equal to or greater than 0.95.

*BEAST inferred maximum clade credibility species tree inferred from 
six nuclear genes and a single mtDNA gene, black and open circles
denote nodes with a Bayesian posterior equal to or greater than 0.95.
The inferred phylogenies are orthodox in the resolution of the two major holocentrid taxonomic groups, Holocentrinae (Squirrelfishes) and Myripristinae (Soldierfishes), as monophyletic; however, two of the three genera of Holocentrinae (Sargocentron and Neoniphon) are dramatically non-monophyletic in these phylogenies. We use the phylogenetic trees to show that many of the characters used to diagnose and delimit these genera have a complex evolutionary history. A new taxonomy for Holocentrinae is proposed where several species previously classified as Sargocentron are treated as species of Neoniphon, Sargocentron is restricted to the least inclusive clade containing S. spiniferum and S. rubrum, and the subgenus Flammeo is elevated to contain F. marianus. Holocentrus is monophyletic in the phylogenies.

These results are exciting, as they indicate that molecular datasets being collected by ichthyologists in the early 21st Century provide well-resolved phylogenies for closely related lineages, as well as the deepest branches in the Actinopterygian Tree of Life (e.g., 11). Also, these well resolved phylogenies reveal substantial incongruence between the formal classifications of species and inferred phylogenetic relationships. Perhaps most exciting are the numerous evolutionary studies, aimed at understanding the mechanisms that have generated the abundant species diversity of fishes, which will be guided by these well resolved species level phylogenies.

References

1.  Maddison, W.P. 1997. Gene trees in species trees. Systematic Biology. 46:523-536.
2.  Edwards, S.V., L. Liu, and D.K. Pearl. 2007. High-resolution species trees without concatenation. Proceedings of the National Academy of Sciences of the United States of America. 104:5936-5941.
3.  Edwards, S.V. 2009. Is a new and general theory of molecular systematics emerging? Evolution. 63:1-19.
4.  Hollingsworth, P.R. and C.D. Hulsey. 2011. Reconciling gene trees of eastern North American minnows. Molecular Phylogenetics and Evolution. 61:149-156.
5.  Kocher, T.D., W.K. Thomas, A. Meyer, S.V. Edwards, S. Paabo, F.X. Villablanca, and A.C. Wilson. 1989. Dynamics of mitochondrial DNA evolution in animals:  amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the United States of America. 86:6196-6200.
6.  Dornburg, A., J.A. Moore, R. Webster, D.L. Warren, M.C. Brandley, T.L. Iglesias, P.C. Wainwright, and T.J. Near. 2012. Molecular phylogenetics of squirrelfishes and soldierfishes (Teleostei: Beryciformes: Holocentridae): reconciling more than 100 years of taxonomic confusion. Molecular Phylogenetics and Evolution. 65:727-738.
7.  Sorbini, L. 1975. Gli Holocentridae di Monte Bolca. II: Tenuicentrum pattersoni nov. gen. nov. sp.  Nuovi dati a favoure dell’origine monofiletica dei beryciformi (Pisces). Studi e Ricerche sui Giaciamenti Terziari di Bolca. 2:456-472.
8.  Sorbini, L. 1979. Gli Holocentridae di Monte Bolca. III. Berybolcensis leptacanthus (Agassiz). Studi e Ricerche sui Giaciamenti Terziari di Bolca. 4:19-35.
9.  Sorbini, L. 1975. Gli Holocentridae di Monte Bolca.  I: Eoholocentrum, nov. gen., Eoholocentrum macrocephalum (de Blainville) (Pisces-Actinopterygii). Studi e Ricerche sui Giaciamenti Terziari di Bolca. 2:205-228.
10.  Stewart, J.D., Taxonomy, paleoecology, and stratigraphy of the halecostome-inoceramid associations of the North American Upper Cretaceous epicontinental seaway. 1984, University of Kansas: Lawrence. p. 201.
11.  Near, T.J., R.I. Eytan, A. Dornburg, K.L. Kuhn, J.A. Moore, M.P. Davis, P.C. Wainwright, M. Friedman, and W.L. Smith. 2012. Resolution of ray-finned fish phylogeny and timing of diversification. Proceedings of the National Academy of Sciences of the United States of America. 109:13698-13703.

Monday, September 3, 2012

An Adaptive Radiation on Ice

 In February of 2012 we published a set of comparative analyses to investigate the adaptive radiation of Antarctic notothenioids, a clade of percomorph teleosts. The authors included a graduate student in my lab, Alex Dornburg, a former postdoc, Kristen Kuhn, the venerable master of Antarctic fishes, Joseph T. Eastman, a former Near Lab Yale undergraduate, Jillian Pennington, my valued Italian colleagues, Tomaso Patarnello and Lorenzo Zane, a fish physiologist from Argentina, Daniel A. Fernández, and my oft partner in high seas Southern Ocean mischief, Christopher D. Jones who was our cruise leader.


Artedidraco skottsbergi (9 cm) collected in the Bransfield Strait.
Photograph by Thomas J. Near
Dissostichus mawsoni,
Antarctic Toothfish
The term adaptive radiation has been applied to very few marine fish lineages. The notothenioids exhibit anti-freeze glycoproteins (AFGP) to avoid freezing in the subzero waters of the Southern Ocean around Antarctica. Antarctic notothenioids exhibit substantial morphological and ecological differences among closely related species, ranging from the pelagic Antarctic Toothfish, Dissostichus mawsoni, which can reach 1.75 m in length, to the entirely benthic Artedidraco skottsbergi that has a maximum size of only 11 cm. All notothenioids lack a swim bladder, the primary buoyancy organ of ray-finned fishes and homologous to our lungs; however, several lineages of notothenioids have evolved modifications of buoyancy through reduction of ossification and lipid deposits. Some notothenioids are neutrally buoyant, meaning they have no weight in seawater. The differences in buoyancy among closely related species is nearly as substantial as differences in their morphology.

The field work for this study encompassed four expeditions (2001, 2003, 2006, and 2009) to the Southern Ocean onboard the Russian research vessel Yuzhmogeologia. On these cruises I was able to make buoyancy measurements from more than 1,000 specimens, and I collected more than 2,000 specimens and tissue samples that are now housed in the fish collection of the Peabody Museum of Natural History.

Eleginops maclovinus, the non-Antarctic sister species to the entire notothenioid 
Antarctic Clade. Maximum size is 90 cm. 
www.viarural.cl/alimentos/pescados-y-mariscos/robalo/robalo.htm
There are approximately 100 species that comprise an unnamed Antarctic Clade that is considered an adaptive radiation, but there are also three species-poor lineages that are early branching and endemic to non-Antarctic cold-temperate near-shore habitats in South America, Falkland Islands (Islas Malvinas), Tristan de Cunha, Australia, Tasmania, and New Zealand. These lineages include Bovichtidae, Pseudaphritis urvillii, and Eleginops maclovinus. These lineages were never exposed to the freezing conditions of the Southern Ocean and provide an important contrast to understand the origins of the adaptations to polar conditions, as well as the ecological and morphological diversity observed in the Antarctic Clade.
Distribution of Eleginops maclovinus
www.viarural.cl/alimentos/pescados-y-mariscos/robalo/robalo.htm

Previous work that I had published, using relaxed molecular clock analyses of mitochondrial DNA rRNA gene sequences, indicated that the Antarctic Clade originated around 24 mya. This is well after the onset of global cooling and appearance of the first Antarctic ice sheets at the Eocene-Oligocene boundary, some 35 mya. Subsequent molecular age estimates using primarily DNA sequence data from nuclear genes have confirmed this result. However, there was no analysis that assessed if Antarctic notothenioids exhibit an explosive diversification subsequent to their origin, a pattern expected in an adaptive radiation.

My colleagues and I investigated the tempo of diversification in notothenioids through analyses of a time-calibrated phylogeny that was inferred from DNA sequences of five nuclear genes (myh6, sh3px3, tbr1, zic1, and the first intron of the S7 ribosomal protein) and two mitochondrial genes (ND2 and 16S rRNA). The phylogenetic analysis included 83 of the approximately 120 recognized notothenioid species.

The inferred molecular phylogeny is quite orthodox, relative to previous inferences from morphological and molecular data. For example, Bovichtidae (containing Bovichtus and Cottoperca) and Pseudaphritis urvillii are successive early diverging non-Antarctic lineages, and the South American and Falkland Island distributed Eleginops maclovinus (pictured above) is the sister lineage of the Antarctic Clade. Within the Antarctic Clade the only noteworthy result is the paraphyly of Nototheniidae, but support for the inferred relationships among the earliest diverging lineages of the Antarctic Clade is limited.

Estimating the ancestral character states of AFGP on the notothenioid time tree supports a single origin of the trait along the branch subtending the most recent common ancestor of the Antarctic Clade. A method that detects changes in lineage diversification rate identified the Antarctic Clade and the common ancestor of Artedidraconidae, exclusive of Artedidraco skottsbergi, as exhibiting high diversification rates relative to the estimated background diversification rate. However, when we performed additional temporal analyses, it was clear that there are pulses of lineage diversification among much younger lineages in the Antarctic Clade. In other words, a shift of diversification rate leading to the Antarctic Clade is consistent with the expectation that AFGP was a trigger to the notothenioid adaptive radiation, we also observed temporal periods of high diversification that are at least 10 million years after the origin of AFGP. It does not seem that the origin of AFGP tells the whole story of the notothenioid adaptive radiation.

It is important to note that unlike any other set of near-shore marine habitats on Earth, the fish fauna of the Southern Ocean is completely dominated by the closely related notothenioids. This was not always the case. A fossil fish fauna from Seymour Island at the tip of the Antarctic Peninsula clearly shows that about 40 mya Antarctica was the home of a temperate and phylogenetically diverse teleost fauna that was not much different from what I can see off shore from New Haven in Long Island Sound. As polar conditions developed in the Southern Ocean this fauna was extirpated, opening up a set of niches that were ultimately exploited by notothenioids. In this paper we propose that the particularly harsh environmental and physical conditions of near-shore habitats in Antarctica, particularly starting about 14 mya, may have led to a cycle of lineage extirpation, recolonization, and diversification within the notothenioid Antarctic Clade. This hypothesis is supported by our finding of pulses of diversification associated with the most species-rich notothenioid lineages (e.g., Artedidraconidae, Trematomus, and Channichthyidae) that correspond to a time around 10 to 5 mya.

Vomeridens infuscipinnis, a species of Bathydraconidae, or dragonfishes.
This species is very light in water, with the lowest buoyancy among measured
bathydraconids. Photograph by Thomas J. Near
Trematomus newnesi, a semi-pelagic species of Nototheniidae
that has an intermediate buoyancy. Photograph by Thomas J. Near
When we examined the pattern of diversification of buoyancy in notothenioids, there is a clear pattern of substantial among clade disparity early in the diversification of the Antarctic Clade, just as expected in an adaptive radiation. However, two of the most species-rich notothenioid subclades, Channichthyidae and Trematomus, show substantial within lineage disparity throughout their respective histories. This indicates that unlike the Antarctic Clade as a whole, closely related species in these lineages are evolving substantial differences in buoyancy.

In this paper we pointed out that regions of the Southern Ocean are among the fastest warming regions on Earth. Such dramatic thermal changes may be cause for concern when considering the future of these cold-adapted fishes. From the perspective of studying the notothenioid adaptive radiation, future work should aim to provide greater phylogenetic resolution among the early diverging lineages of the Antarctic Clade, assess the relationships between habitat and dietary resource utilization, and continue to refine our understanding of species diversity in the clade. Notothenioids are a most fascinating lineage of animals and the fact they are fishes just adds that much to their allure and ensures that we will be paying attention to them for the foreseeable future.

Tuesday, August 28, 2012

A Facebook Conversation



  • Below is a conversation on Facebook started by my colleague Frank Pezold in response to my first posting on the Fish Phylogenetics blog.  For those who may not know, there is a group of ichthyologists that are not pleased with the use of data matrices and optimization methods for the inference of phylogenetic relationships. Really, this is not a joke.

    These systematists are particularly displeased with the use of molecular data in these efforts and are concerned that "molecular classifications" will make systematic ichthyology irrelevant.

    While the concern is pointed at the ichthyological taxonomic discipline, it actually represents a fringe element of the phylogenetics community that continues to advocate three taxon analysis. Also, from a wholly misinformed perspective, they refer to data matrix driven phylogenetics as "phenetic." 

    Let me note that this perspective has absolutely no traction in the mainstream field of phylogenetics. These papers are not being published in Systematic Biology, and it is unlikely they ever find a larger audience. My guess is that this very narrow view of phylogeny is maintained in ichthyology because we do not have a well-resolved set of phylogenetic hypotheses that includes the diversity of all living teleost lineages. Once such a set of phylogenies are available, I suspect these views will retreat from the landscape of practicing phylogenetic ichthyology. It is important to note, as is obvious in reading these comments, that a resolved phylogeny of teleost fishes is not a goal of these systematists.

    I think that we as phylogenetic ichthyologists will continue to remain irrelevant if we are not able to articulate the relationships of teleost fishes to the broader community of scientists attempting to resolve the entire Tree of LIfe.

    The conversation is posted just as it appeared on Facebook.


    Frank Pezold Nice site Thomas. I have a comment on this comment - "Much of what has constrained the development of ray-finned fish phylogenetics is been the reluctance of many ichthyologists to whole heartedly incorporate molecular data (e.g. DNA sequence data) in their efforts to infer phylogenetic relationships." I think the difficulty primarily arises from speedy conversions of molecular phylogenies to classifications, which can be fraught with problems much discussed, and the reduction of information available in morphological studies to a simple overlay on a molecular phylogeny instead of its use as another dataset. neither of the problems is attached to this publication...it offers an independent analysis that has resulted in significant phylogenetic insight.
    August 24 at 12:53pm ·  · 3

  • Thomas Near Frank, thank you for the comment. You should post this on the blog, where I can provide a longer response. What I will say here is that I rather see speedy conversions of molecular phylogenies to classifications than the continued recognition of para- and polyphyletic groups in the established classification.
    August 24 at 1:06pm ·  · 1

  • Frank Pezold there is a middle ground i think that doesnt require the adoption of the latest hasty and often incomplete analysis yet doesnt rest forever on the rump of a stodgy ignorance of the value of molecular tools. I also fear that much of the housekeeping left behind the wash of the molecular systematic wave will be left to us older doffs or just left behind period. i'll check in on the blog, but for the moment this has more readers, and it is on my radar. glad to see all of this - the paper and discussions online.

  • Thomas Near Can you cite some examples?

  • Frank Pezold Of what, the fact that the two ends of an extreme are joined by a continuum?
    Saturday at 9:34pm via mobile · 

  • Thomas Near No, hasty changes to classifications.

  • Frank Pezold Of proposed classifications, sure, but I thought the question here was of philosophical approach.
    Saturday at 9:39pm via mobile · 

  • Anthony Gill ‎"...I rather see speedy conversions of molecular phylogenies to classifications than the continued recognition of para- and polyphyletic groups in the established classification." This implies that the molecular methods are somehow retrieving truth ... or perhaps that morphological studies are not questioning "established classification." Neither is true. The essence of systematics is understanding characters (homologues) and their distributions ... something that is not generally tracked in molecular studies (only phylogenies and statistics are presented). Rapid changes in classification from studies (morphological or molecular) that do not make a serious attempt to understand characters are unlikely to be a good thing. More comments on this (and the fate of molecular classifications) is given here:http://www.mapress.com/zootaxa/2010/f/zt02450p040.pdf
    Sunday at 10:13pm ·  · 1

  • Thomas Near I said neither. That is what you want to see. No one who practices phylogenetics and realizes that the science is based on inference thinks they are revealing "truth" when they present any phylogenetic hypothesis. The whole meme that molecular phylogenies do not track the character distributions is at best tired, and at worst disingenuous. One can take the phylogenetic tree that represents an optimal distribution of character stats and the data (phenotype or DNA sequences) to assess character support. There is not enough printed space in a typical journal article to map the character changes. Also, any statement that these phylogenies are not the result of optimal character state distributions is uninformed. Yes tress and support are presented...in every phylogenetic field in the early 21st Century. We can pine for the glorious days of gas-lit streets, but those days are past. So are noteworthy phylogenetic studies that sample 8 taxa for 30 characters. As for classification, I would still prefer the "rapid changes" to the clearly wrong aspects of teleost classification that everyone knows are not supported by available data (e.g., Protacanthopterygii and Perciformes), but are maintained because of some unspoken standard that is required to change the revered tablets handed down by Regan, or from the shear force of personality for particular pet hypotheses (e.g., Johnson and Smegmamorpha). Ichthyology is in a crisis, not because of molecular inferred phylogenies and rapidly changing classifications, but rather our crisis is tied in our inability to articulate our work in the context of 21st Century phylogenetics. We have the most difficult problems in the Vertebrate Tree of Life, but we fail to capitalize on these interesting questions to get systematists in other organismal disciplines interested in our work. Instead of using the best tools available, we squabble while the largest polytomy (Percomorpha) in the Ray-Fin Tree of Life remains unresolved.

  • Anthony Gill Yes, inference it is. But I see words like "resolved" thrown around in recent molecular papers, which suggests that truth has been revealed. I see the current emphasis on phylogenetic trees (solutions to data sets) and statistics as at odds with character driven investigation. Current molecular phylogenetics (and other optimization approaches) do not simply track character distributions, they create them. Character conflicts in the original observations are reinterpretted as new characters and evidence for new relationships. I do not see an obvious compromise, because it seems that the different approaches have different goals (which is not to say that they won't sometimes deliver the same relationships). One is an investigation of character evolution (and driven by particular models of evolution), while the other is an investigation of character distribution and classification (a pattern approach). Perhaps I am from the days of gas lights (though the light source for my microscope is LED), but I often find more worth in an overlooked paper by Theodore Gill than in the latest phylogeny and classification of x or y, because Gill described characters that could be reinvestigated. Gill's contributions in the long run was not his classifications or his suggested relationships, but the evidence that formed the basis of his classifications. This is not to say that our existing classification system is perfect and there is no shortage of dogma (I commented on the Paracanthopterygii and Perciformes problems nearly 20 years ago), but simply creating a plethora of short-lived new ones is likely to make our field irrelevant.
    Yesterday at 12:23am ·  · 1

  • Thomas Near No words are being thrown around, they are chosen carefully. This is reflective of the fact that some of these papers are coming out in the most difficult journals to have one's work published. I see the word resolution as relating to the ability to strongly discriminate among alternative answers given a particular model and set of data. It is your suggestion that resolution means truth, not mine nor is it the unambiguous definition of the word in the OED. If you are at odds with the current state of affairs in phylogenetics, then your target needs to be much more inclusive than ichthyology. Even when ichthyology catches up with the other vertebrate disciplines in the sophistication of its phylogenetic work, we as ichthyologist will still maintain our connection to previous workers through our excellent approach to scholarship. Yes, even a molecular systematist can appreciate your overlooked paper by Gill and the character information it contains. I would also posit that molecular characters can, and often are, reinvestigated. Molecular data is very fine evidence for phylogenies, and hence any classifications that would follow from those phylogenetic perspectives. There appears to be an odd perception that molecular data is not evidence. It is. Even if a worker does not map their characters on the trees, it is still evidence. I appreciate your comments on groups like Paracanthopterygii and Perciformes; however, there they are, still ensconced in some of the most referenced teleost classifications. Let's stop beating around the bush. Tell me if morphological data is ever going to result in a resolved phylogeny for let's say 500 percomorph species sampled from more than 200 taxonomic families. If this is possible, when will it happen?

  • Anthony Gill As I said, different goals.

  • Thomas Near So a goal of yours as a systematist is not resolution of the Tree of Life?

  • Prosanta Chakrabarty Tom, please cut and paste this discussion on the new blog, so that the discussion is preserved - hopefully it can continue there
    23 hours ago · 

  • Prosanta Chakrabarty Anthony GillFrank Pezold, please like this or the above comment to give Thomas Near permission to repost this discussion to the phylogenetics blog.
    23 hours ago ·  · 3

  • Luiz Rocha Yes, would be great to have this discussion preserved and extended...
    22 hours ago ·  · 2

  • Rodrigo Torres Niiice!
    22 hours ago · 

  • Anthony Gill I see a large number of goals in your post Tom, many of which are sociological rather than scientific. My goal as a systematist is as it has always been: to continue to develop a natural classification of fishes through improved understanding of characters and their distribution. My understanding of character distribution is based on a meagre collection of around 800 species (about 2,500 specimens) representing about 150 acanthomorph families, but with reference to a much broader literature-based survey across fishes - supplemented with about 30 years of direct observation of specimens. My goal is to diagnose groups - natural classifications - not ancestral conditions at nodes. That, in a nutshell, is the fundamental difference in our goals. I see no particular need to repost my comments elsewhere, or really to devote more time to any discussion.
    17 hours ago · 

  • Thomas Near No sociology here. Just wanting to know how teleosts are related and their divergence times. If you truly have a 800 species dataset, you should publish that in a comprehensive paper. It would be a wonderful and impactful contribution to the field of systematic ichthyology. You may retort that you published that data in various papers, but it would be nice if you had an ambition for a grand synthetic work. This is reflected by the fact that I was not aware of your incredible dataset because it has never, to my knowledge, been published in one piece of work. By the way, monophyletic groups are the basis of natural classifications for 99% of practicing systematists. I guess you are are a "one percenter." Please excuse my light-hearted joke. It is meant to reflect that fact that all of us ichthyologists are in the same boat.
    16 hours ago · 

  • Anthony Gill It is obvious again that we are not on the same page. There is no dataset as such, because that is not how morphological systematics has progressed. The mention of the specimens (which only refers to skeletal preps on my lab bench - there is a similar set available for study at ASU, and I also based many observations on skeletal preps in the NHM, AMNH and USNM) is simply to contrast how we contribute (and that we do not indeed have the same goals). You challenged morphologist to produce a topology based on 500 species across 200 percomorph families, because that is the only way molecular studies can contribute (at least while attention is solely on topologies rather than characters): each topology is a solution to a given dataset, which stands in isolation from future or past solutions. In their quest for understanding characters and their distribution, morphologists routinely refer to much larger "datasets" - specimens (the only realities we actually deal with) and literature (which may guide us to examine other specimens). I could easily amass a huge number of characters that spanned specimens available to me for study, but many of those characters would be poorly defined and not representative. (I could easily populate it a matrix with fin-ray and scale counts, for example.) The emphasis, instead, is on trying to clearly define characters and understand their distribution. It is not merely about large numbers of characters - is the weberian apparatus not adequate to diagnose a group of fishes? You are correct in putting me in a 1% minority, however, in that I am convinced the current emphasis on optimization methods is problematic. It is not that I do not recognise natural groups as monophyletic, but for me monophyly indicates that two or more taxa are more closely related to each other than another taxon outside the monophyletic group. Refences to processes and ancestors (or ancestral characters) lie outside our field of observation, and may actually impede rather than assist in developing an understanding of relationships. I acknowledge also that I am unlikely to make a grand contribution to the tree of life. I am in a non-research position doing research in my spare time supported out of my own pocket. However, I hope I can make a lasting contribution to what I see is the essence of systematics - the understanding of characters and their distribution. It is these and not ever-changing topologies that matter to me. I'm afraid that same limiting resource (spare time) is why I cannot continue to dedicate time to this discussion, or to pursue it on other portals.
    14 hours ago ·  · 1

  • Prosanta Chakrabarty Tony, you don't need to continue the discussion if you don't want to, but please grant permission to post this on the original blog so that a broader group can see it and it can be saved in a better place.
    13 hours ago via mobile · 

  • Anthony Gill Okay, go ahead.
    13 hours ago · 

  • Thomas Near I think it is funny that you are turned off by "ever changing topologies" when that is the essence of inferential science, changing hypotheses with the addition of data. Given that the node which subtends nearly 17,000 percomorph species is currently a polytomy, we are facing a period of flux. Going from a polytomy to any resolved solution is a change. I am confident that the ambitions of us who hope to bring systematic ichthyology into the 21st Century will be realized. Please continue to contribute your views, as all voices in our science are welcomed and appreciated.
    13 hours ago · 

  • Frank Pezold This has been very interesting but I think we have drifted a little from the spark that lit the conversation. It has to do with the responsibility we have to users of our information (those outside of the circle of systematics). Working from morphological studies systematists would amass data, as Tony describes, and periodically publish a tome sometimes in concert with data collected by others. This usually took significant time and much was vetted in talks prior to the publication. Molecular data is much more quickly gathered and processed and this has led to rapid publication of new hypotheses - whether of species or phylogenetic relationships. A major concern I feel is that we don't have the same period of vetting and whether it is a question of what constitutes a species or a higher taxon, we have an often fluid vision of relationships (dependent on the particular gene or the limits of taxon sampling) that can change quickly. It is not a question of whether or not one dataset is better than another - we need all the data we can get while of course weeding out irrelevant data from either set. We just need to show some sense of responsibility when we share our results. Otherwise we trivialize our work and cheapen the role of the systematist in evolutionary biology. I found the work shared on this post informative and look forward to more from the authors as well as insights we will obtain from the information Tony is gathering.