Ichthyology Lecture # 3 Systematics, taxonomy and classification schemes

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1 In all probability more paper has been consumed on the questions of the nature and definition of the species than any other subject in evolutionary and systematic biology. E. O. Wiley Ichthyology Lecture # 3 Systematics, taxonomy and classification schemes

2 Describing and classifying the diversity of life and postulating how that diversity arose-are fundamental activities of biology. The heart of this course is the diversity of fishes, including evolutionary relationships among major groups of fishes.

3 Lest you think this has all been worked out-you only have to pick up a recent scientific journal dealing with taxonomy and systematics to the see the articles. Edward Drinker Cope Copeia -- named for 19 th century naturalist and paleontologist Edward Drinker Cope-is the primary outlet for publication of taxonomic and systematic findings for fishes, reptiles and amphibians, amd is published by the American Society of s and s

4 Today s Objectives Understand basic concepts underlying: taxonomy basic tools and rules for naming species classification importance of distinguishing ancestral v. derived characteristics systematics differences between major approaches for investigating evolutionary relationships and why these are working hypotheses

5 Today s Objectives Understand basic concepts underlying: taxonomy basic tools and rules for naming species classification importance of distinguishing ancestral v. derived characteristics systematics differences between major approaches for investigating evolutionary relationships and why these are working hypotheses

6 In all probability more paper has been consumed on the questions of the nature and definition of the species than any other subject in evolutionary and systematic biology. E. O. Wiley 1978 Species are the fundamental unit of classification schemes, with more than 20 concepts of species

7 Biological Species Concept Ernst Mayr introduced in 1942 "species are groups of interbreeding natural populations that are reproductively isolated from other such groups."...is problematic

8 What is a species? biological species concept, (reproductive isolation concept): groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups. all individuals of a population like the Devils {the BSC} would also only Hole account Pupfish for a trivial amount of diversity, and is likely the worst concept that any OR different kinds of organisms living in the area of biology should adopt. Mayden 2002 same area

9 British ichthyologist C. Tate Regan defined a species as a group of organisms with distinctive enough morphological characters that, in the opinion of a competent systematist, are sufficiently definite to entitle them to a specific name The definition of a MORPHOSPECIES does not depend on evolutionary concepts

10 Son of a Clergyman in Rural Sweden Prominent Botanist and Natural Historian Linnaeus revolutionized the way in which scientific names are applied to plants, fungi, and animals in his 1753 publication, Species plantarum using a latinized binomial (two names) species name [Genus species] Prior to Linnaeus, the names used by scientists to designate particular kinds of plants were whole phrases, such as "annual, much-branched Physalis, with strongly-angled, glabrous branches and leaves with sawtoothed edges." The Linnaean binomial for the same plant is simply Physalis angulata. Systemae Naturae grew from 11 pages in the first edition in 1735 to over 3,000 pages covering some 15,000 species in the 13 th edition of 1770 Carl Linneaus

11 This classification of taxa was a hierarchical system (Kingdoms, classes, orders, genera and species) based on observable characters-taxon is a group of organisms given a name According to Linneaus, the SPECIES as a taxon is a naturally occurring entity, immutable and not subject to change. Linneaus and his colleagues (100 years before Darwin) based their classifications on morphology. Carl Linneaus 'Classis et Ordo est sapientiæ, Species naturæ opus' [Class and Order are the work of human wisdom; Species is the work of nature] "Deus creavit, Linnaeus disposuit,"

12 Taxonomy - involves recognizing and describing biodiversity and arranging the described biodiversity into a classification scheme. Species descriptions are governed by ICZN Species description must include a valid (not occupied) binomial name type specimen(s) - Holotype, Paratype type locality diagnosis an illustration and it must be published Typological thinking, immutability of a species if a specimen is found that is slightly different-it could be described as a new species. International Code of Zoological Nomenclature (for animals) Codified: Stability, universality, permanence.

13 For example: Percina crypta, new species Halloween darter Figure 2 Holotype. GMNH 21606, male, 69.7 mm SL, Georgia, White County, Chattahoochee River at GA Hwy 17/75 at Nacoochee, Georgia (Nora Mill), 11.1 air km NNE Cleveland, 17 May 1994, B. J. Freeman,. Paratopotypes. GMNH (18; mm), Collected with the holotype. Paratypes. Georgia: Lumpkin County: GMNH (1; 58 mm) Chestatee River at and alongside GA Hwy 60, 3.7 km S of Dahlonega, 30 October 1996; Diagnosis. Percina crypta differs from all other described species of Percina in possessing the following combination of characters:... Percina crypta is most readily distinguished from sympatric P. nigrofasciata in having narrowly separated dark dorsal saddles Freeman, M. C., B. J. Freeman, N.M. Burkhead, and C. A. Straight A new species of Percina (Perciformes: Percidae) from the Apalachicola River drainage, southeastern United States. Zootaxa1963:

14 International Code of Zoological Nomenclature (for animals) ICZN was founded in Its task is to create, publish and, periodically, to revise the International Code of Zoological Nomenclature. The Commission also considers and rules on specific cases of nomenclatural uncertainty. These rulings are published as 'Opinions' in the Bulletin of Zoological Nomenclature. The Code is not static- see ZT_ICZNproposal_Epublication.pdf, regarding proposed amendment to the code to cover electronic publication, and what does and does not constitute publication also-iczn rules a farewell to Tubificidae (Annelida, Clitellata) THESE ARE AVAILABLE ON WETPAINT SITE UNDER Resources/Selected Readings... Article 26-the tenth edition of Linne s Systema Naturae, 1758, is the work which inaugurated the consistent application of the binary nomenclature in zoology. The date 1758, therefore, is accepted as the starting point of zoological nomenclature and of the Law of Priority.

15 in spite of the CODE-establishing stability can be messy and murky-and species have BEEN discovered and formally described several times-i ll use and example well known to everyone--the Striped Bass Morone saxatilis (Walbaum) the derivation of the genus is unknown, but the trivial epithet means rock dweller. Note the authors name in parentheses -indicating the species was placed in a different genus than the one originally described by the Author first described by Johann Julius Walbaum (MD in Germany). Type Locale NewYork, USA as Perca saxatilis. He named over 200 species but his style--lack of types, poor descriptions, almost no illustrations and no type locality for most species-relegated almost all of his species to obscurity! 1814, S.N. Mitchell (another physician) also described the striped bass as Roccus striatus, in a report on the Fishes of New York. Mitchell also described what we now know as a related species, placing it in the genus Morone. The Law of Priority of the Zoological Code means that the older name is the valid one, although the genus is wrong-the striped bass is not a perch, but Walbaum s work had apparently been forgotten.

16 Also ignored in a revision of relationships, Pieter Bleecker (a prolific Dutch MD who mostly explored fishes in Indonesia describing 1925 spp, 40% of which are still valid) synonomized Roccus with Morone. At some point, the saxatilis was returned to the striped bass, but as a species of Roccus. When it was discovered that Morone had priority over Roccus, a rule called Nomen oblitum was invokedwhich says that if a name has not been used since 1899, AND the synonym HAS been used by at least 10 authors in at least 25 works in the past 50 years-the OLDER NAME is qualified as Nomen oblitum- forgotten. Francis Hemming the distinguished lepidopterist and Secretary for the ICZN was offended that the Law of Priority had given way to the Nomen oblitum rule, and packed the gallery of the Commission meeting in 1953, and browbeat the commission into changing the name back to Morone. Morone saxatilis is the valid name today! A bit esoteric, perhaps, but names often change, in accordance with rules. Species names are governed by the Law of Priority, but with variances like Nomen oblitum meant to enhance stability of names.

17 1792: Perca saxatilis Walbaum 1814: Roccus striatus Mitchell Law of Priority 1876: Bleeker synonomized Roccus with Morone 1900 s: R. striatus, R. lineatus., R. saxatilis all used! mid-20th century: ICZN - Morone saxatilis correct but nomen oblitum Many authors continued to use Roccus instead of Morone, and in 1966 Whitehead and Wheeler demonstrated the priority of Morone over Roccus. Striped bass Morone saxatilis (Walbaum)

18 in 1988, many of us were shocked and surprised to learn that our beloved rainbow trout Salmo gairdneri Richardson was actually an Asian species Oncorhynchus mykiss (Walbaum)

19 1740, Georg Wilhelm Steller described the Pacific salmons, including mykyhs which...tastes better than any other fish on Kamchatka, except for the king salmon Steller died in 1746 before his publication which described 6 species could be published Steller s work was translated into Russian from German in 1755, then into English in 1764, into French in 1768 and finally in 1792 was published by WALBAUM as Salmo mykiss Richardson, in 1836 described it as Salmo gairdneri. a review of the taxonomic history of mykiss and gairdneri found them closely related and recent genetic studies found differences to be within intraspecific variation finally, in 1988 Smith and Stearley proposed that these were actually the same species at an ASIH meeting and this was published in Fisheries in Much furor ensued for a few years

20 Megamouth shark Classification and Systematics Megachasma pelagios Taylor, Compagno & Struhsaker Family Megachasmidae Classification is putting things into groups when a taxonomist describes a new species, he/she must do some classification-the new taxon is either grouped with other species in an existing genus, or it is placed in an entirely new genus...and perhaps family as in the case of the megamouth shark, described in 1976 as Megachasma pelagios in a new Family Megachasmidae-asserting that the species does not belong to any existing genera

21 Classification - putting things into groups species description - some level of classification is inherent but a phylogeny is (phylogenetic relationships to other taxa) not required Systematics - study of phylogenetic (evolutionary) relationships among species or higher taxa as a basis for classifications hypotheses for evolutionary processes

22 MAJOR OBJECTIVE OF CLASSIFICATION SCHEMES IS TO DETERMINE WHO IS RELATED TO WHOM AND HOW CLOSELY That classification is considered most natural that best reflects the evolutionary relationships of the organisms involved i. e., it is correct

23 2nd objective: System serves for convenient information storage and retrieval (can be used easily and modified when new info becomes available) i.e., it s useful The system has to be both correct and useful

24 * Traditional Evolutionary Systematics 1. Use Intuition to Select characters believed to reflect ancestry; 2. Look at fossil record for clues; 3. Don t mistake convergence for homology; 4. Draw a tree (phylogram) * Evolutionary classification: descent with modification Problem-can obtain different classification if you use different characters, not transparent what the rules are or how to test classification

25 Mullet, a primitive spiny-rayed teleost = homoplasy Similarities due to convergence, not homology! Cuda, an advanced spiny-rayed teleost

26 Phenetics = Numerical taxonomy Use data for lots of characters* to estimate mathematically total similarity between organisms *Meristics = countable traits; *Morphometrics = measurable traits operational taxonomic units (OTUs) phenogram

27 Willi Hennig, introduced Cladistics, or phylogenetic systematics His monograph of 1950 was only translated into English in An entomologist, he divided characters into two groups-apomorphies [recently evolved, derived or advanced characters] AND Plesiomorphies [more ancestral, primitive or generalized characters]. The goal is to find Synapomorphies that diagnose monophyletic groups or CLADES [groups containing an ancestor and all its descendant taxa]. Symplesiomorphies [shared primitive characters] do not provide useful data for constructing phylogenetic classifications because these primitive characters may be retained in distantly related taxa, and may also be present in advanced taxa. Autapomorphies, specialized characters present in only a single taxon, are important in defining that taxon, but useful in constructing a phylogenetic tree

28 CLADISTICS (phylogenetic systematics) derived derived ancestral derived ancestral derived CHANGE CHANGE *shared, derived characters!

29 L S G B T bony scales enamel on teeth jaws jaw & throat bones Lampreys Sturgeons Gars Bowfins Teleosts notochord

30 SOME CLADISTICAL TERMS YOU NEED TO KNOW CLADE AN ANCESTOR PLUS ALL ITS DESCENDANT GROUPS. APOMORPHY A DERIVED (I.E. RECENTLY EVOLVED) TRAIT. SYNAPOMORPHY A SHARED, DERIVED TRAIT (ONE SHARED BY ALL MEMBERS OF AN ADVANCED CLADE). PLESIOMORPHY AN ANCESTRAL TRAIT. SYMPLESIOMORPHY AN ANCESTRAL TRAIT SHARED BY ALL ANCESTORS. MONOPHYLETIC LINEAGE A GROUP OF RELATED ORGANISMS THAT SHARE A COMMON ANCESTOR (A GROUP IS MONOPLYLETIC IF EVERYBODY SHARES AN ANCESTOR, I.E. IS A TRUE CLADE). DERIVATIONS REFER TO TRAITS THAT HAVE CHANGED IN A GROUP DURING ITS EVOLUTION. A DERIVED TRAIT IS ONE THAT IS DIFFERENT FROM THE ANCESTRAL CONDITION. ROUGHLY: ANCESTRAL=PRIMITIVE (=GENERALIZED) ADVANCED=DERIVED (=SPECIALIZED) Monophyletic = natural

31 ARTIFICIAL GROUPS? PARAPHYLETIC - does not contain all the descendents of a single ancestor e.g., fishes fossil fishes + jawless fishes + sharks & rays, relatives + coelacanths and lungfishes + ray-finned fishes who s missing? we are!

32 Classes: Placodermi {extinct} Chondrichthyes Cartilaginous fishes Superclass Gnathostomata Acanthodii {extinct} Jawed vertebrates Sarcopterygii Lobe-finned fishes, tetrapods Actinopterygii Ray-finned fishes

33 ARTIFICIAL GROUPS? PARAPHYLETIC - does not contains all the descendants of a single ancestor e.g., fishes POLYPHYLETIC - does not include the common ancestor e.g., homeotherms = birds and mammals Amphibia Mammalia Testudines Lepidosauria Crocodylia Aves Archosauria Diapsida Reptilia Amniota Tetrapoda

34 ICHTHYIL- LITERACY OF THE DAY

35 Actual download from Wikipedia, for polyphyletic:?!? Pisces Amphibia Mammalia Testudines Lepidosauria Crocodylia Aves Superclass Gnathostomata Jawed vertebrates Classes: Placodermi Chondrichthyes Acanthodii {extinct} Sarcopterygii Lobe-finned fishes, tetrapods Actinopterygii Archosauria Diapsida Reptilia Amniota Tetrapoda Vertebrata Surf at your own risk

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37 RECEIVED 1/9/2008 ON VERTEBRATE PALEO LISTSERVE I agree with Joe and Tim and several other respondents to DinoGeorge's rant. Apparently, no one on this list except Dan Chure and I HAVE been in this profession long enough to remember the bad old days in the 1960s and 1970s BEFORE cladistics came to dominate systematics. Systematics had no real "method" then, just vague ideas laid down by Simpson and Mayr, and no way for someone to evaluate the hypotheses of the "expert" with their phylogenies that lacked a testable set of characters (or any data at all,for that matter). Then when cladistics came along in the 1970s, Dan and I and everyone else doing systematics at the AMNH heard the same invalid arguments that DinoGeorge raised. Sure, a lot of old assumptions and comforting ideas had to be re-evaluated, but instead of vague "phylogenies" with no data or testability, we finally had something that could be tested. And with this idea came the realization that we were being too smug and self-confident about final "truth": all science has to be testable, and the unsupported assertions of "experts" are not testable science. Sure, there were many false starts and instability in the cladograms, especially in the early stages of cladistic analysis of groups, but I look back at almost 40 years of work now, and it's amazing how many previously insoluble issues have now been resolved.

38 Cladistics provides hypotheses about the relationships of taxa based on the distribution of shared, derived characters, rather than on overall similarity

39 Aggression Lose legs, lose aggression, add levity Fishy shape Lettering 2. Black infill Legs 3. Hypothesis! Test with additional characters, taxa

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41 Back to the question, What are species? evolutionary species concept: a single lineage of ancestral-descendant populations of organisms which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate species are lineages that maintain their independence from other lineages and participate in natural processes all monophyletic supraspecific taxa begin as a single species

42 Operationally [Species] are scientific hypotheses regarding the existence of a unique and distinct biological and evolutionary entity. They are hypotheses presented on the basis of evidence that lead skilled researchers in systematics and taxonomy to propose that some populations are unique and form independent lineages relative to other populations traditionally grouped with them. Mayden 2002 Not typological in concept In practice - divergence in characters provides evidence of independent lineages

43 TABLE 1. Alternative contemporary species concepts (i.e., major classes of contemporary species definitions) and the properties upon which they are based (modified from de Queiroz, 2005). Properties (or the converses of properties) that represent thresholds crossed by diverging lineages and that are commonly viewed as necessary properties of species are marked with an asterisk (*). Note that under the proposal for unification described in this paper, the various ideas summarized in this table would no longer be considered distinct species concepts (see de Queiroz, 1998, for an alternative terminology). All of these ideas conform to a single general concept under which species are equated with separately evolving metapopulation lineages, and many of the properties (*) are more appropriately interpreted as operational criteria (lines of evidence) relevant to assessing lineage separation. Species concept Property(ies) Advocates/references Biological Interbreeding (natural reproduction resulting in Wright (1940); Mayr (1942); Dobzhansky (1950) viable and fertile offspring) Isolation 9 *Intrinsic reproductive isolation (absence of Mayr (1942); Dobzhansky (1970) interbreeding between heterospecific organisms based on intrinsic properties, as opposed to extrinsic [geographic] barriers) Recognition 8 *Shared specific mate recognition or fertilization Paterson (1985); Masters et al. (1987); Lambert and system (mechanisms by which conspecific Spencer (1995) organisms, or their gametes, recognize one another for mating and fertilization) Ecological 7 *Same niche or adaptive zone (all components of VanValen (1976); Andersson (1990) the environment with which conspecific organisms interact) Evolutionary Unique evolutionary role, tendencies, and Simpson (1951); Wiley (1978); Mayden (1997) historical fate (some interpretations) 6 *Diagnosability (qualitative, fixed difference) Grismer (1999, 2001) Cohesion Phenotypic cohesion (genetic or demographic Templeton (1989, 1998a) exchangeability) Phylogenetic Heterogeneous (see next four entries) (see next four entries) Hennigian Ancestor becomes extinct when lineage splits Hennig (1966); Ridley (1989); Meier and Willmann (2000) Monophyletic 5 *Monophyly (consisting of an ancestor and all of Rosen (1979); Donoghue (1985); Mishler (1985) its descendants; commonly inferred from possession of shared derived character states) Genealogical 4 *Exclusive coalescence of alleles (all alleles of a Baum and Shaw (1995); see also Avise and Ball given gene are descended from a common (1990) ancestral allele not shared with those of other species) Diagnosable 3 *Diagnosability (qualitative, fixed difference) Nelson and Platnick (1981); Cracraft (1983); Nixon and Wheeler (1990) Phenetic *Form a phenetic cluster (quantitative difference) Michener (1970); Sokal and Crovello (1970); Sneath Genotypic cluster (definition) SC 2 1 *Form a genotypic cluster (deficits of genetic intermediates; e.g., heterozygotes) and Sokal (1973) Mallet (1995) Species Concepts and Species Delimitation, DeQueiroz Syst Biol 56(6)

44 2 Species Gray Zone vs. 2 species) 1 Species SC9 SC8 SC7 SC6 SC5 SC4 SC3 SC2 SC1 FIGURE 1. Lineage separation and divergence (speciation) and species concepts (after de Queiroz, 1998, 1999, 2005a). This highly simplified diagram represents a single lineage (species) splitting to form two lineages (species). The gradations in shades of gray represent the daughter lineages diverging through time, and the horizontal lines labeled SC (species criterion) 1 to 9 represent the times at which they acquire different properties (i.e., when they become phenetically distinguishable, diagnosable, reciprocally monophyletic, reproductively incompatible, ecologically distinct, etc.). The entire set of properties forms a gray zone within which alternative species concepts come into conflict. On either side of the gray zone, there will be unanimous agreement about the number of species. Before the acquisition of the first property, everyone will agree that there is a single species, and after the acquisition of the last property, everyone will agree that there are two. In between, however, there will be disagreement. The reason is that different contemporary species concepts adopt different properties (represented by the horizontal lines) as their species criteria that is, as their cutoffs for considering a separately evolving lineage to have become a species. Unified Species Concept existence of any of the criteria can be considered as evidence for supporting lineage separation--that is species only the absence of ALL criteria can be considered as evidence against lineage separation Species Concepts and Species Delimitation, DeQueiroz Syst Biol 56(6)

45 The PhyloCode is a formal set of rules governing phylogenetic nomenclature. It is designed to name the parts of the tree of life by explicit reference to phylogeny. The PhyloCode will go into operation in a few years, but the exact date has not yet been determined. It is designed so that it may be used concurrently with the existing codes based on rank-based nomenclature (ICBN, ICZN, etc.). Rank based codes such as ICZN define taxa using a rank (genus, family,etc) and in many cases a type specimen, in contrast, Phylocode does not use ranks to define taxa- the taxa are delimited using a definition based on phylogeny. Thus the content of a phylogenetically defined taxon relies on a phylogenetic hypothesis.

46 The Botanical Review 69(1) January-March 2003 Xfy 6la %I J Just say NO to the Phylocode DeQueiroz, Syst. Biol. 55(l): , 2006 Published Quarterly by The New York Botanical Garden.

47 LINNAEAN CLASSIFICATION TREE GENUS SPECIES Homo sapiens [Humans] Boa constrictor [Boa constrictor] Alligator mississippiensis [American alligator] Passer domesticus [House sparrow] PHYLOCODE TREE sapiens Linnaeus 1758 [Humans] constrictor Linnaeus 1758 [Boa constrictor] mississippiensis Daudin 1801 [American alligator] domesticus Linnaeus 1758 [House sparrow] FAMILY ORDER Hominidae Primates Boidae Squamata Crocodylidae Crocodilia Passeridae Passeriformes Homo Hominidae Primates Boa Boidae Squamata Alligator Crocodylidae Crocodilia Passer Passeridae Passeriformes Aves CLASS Mammalia Reptilia Aves Mammalia Lepidosauria Archosauria Reptilia PHYLUM Chordata Tetrapoda Chordata

48 Near et al. IN PRESS in Systematic Biology have presented a phylogenetic classification of darters based on mitochondrial and nuclear genes