3.7: Assignment- Morphological Phylogenetics - Biology

3.7: Assignment- Morphological Phylogenetics - Biology

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You have returned to college to become a phylogeneticist. One of the first things you wish to do is determine how mammals, birds, and reptiles are related.

Like any good scientist, you need to consider all available data objectively and without a preconceived “correct” answer. In pursuit of that, you should produce a phylogenetic tree based only on morphological features that show birds and mammals are more closely related. You will then produce a totally different tree, also using morphological features, that shows birds and reptiles are more closely related. Do not forget to include all three groups in both your trees.

Based solely off the trees you produce, which relationship would you consider the more likely and why? Once you have answered that question, provide a brief summary of the “modern” understanding of the relationship between these three groups.

Rubric: Morphological Phylogenetics

Mammalian/avian tree is providedTree includes full relationship with all 3 groups sharing multiple characteristics until the mammal/bird split from reptilesTree includes relationships between all 3 groups on a minimal number of featuresTree does not include all 3 groups3 pts
Reptilian/avian tree is providedTree includes full relationship with all 3 groups sharing multiple characteristics until the reptile/bird split from mammalsTree includes relationships between all 3 groups on a minimal number of featuresTree does not include all 3 groups3 pts
One tree is identified as most likelyDiscussion outlines multiple features for the “chosen” treeDiscussion outlines at least 1 reason for the chosen treeDiscussion does not use the trees to argue for a closer relationship3 pts
Modern understanding is discussedAt least 2 pieces of modern evidence (not only morphological) is discussedModern evidence is discussedModern evidence is not discussed or the current relationships are not properly identified3 pts
Total points: 12

Logical basis for morphological characters in phylogenetics

Systematists have questioned the distinction between characters and character states and their alignment with the traditional concept of homology. Previous definitions for character and character state show surprising variation. Here it is concluded that characters are simply features expressed as independent variables and character states the mutually exclusive conditions of a character. Together, characters and character states compose what are here termed character statements. Character statements are composed of only four fundamental functional components here identified as locator, variable, variable qualifier, and character state, and these components exist in only two patterns, neomorphic and transformational. Several controversies in character coding and the use of “absent” as a character state are understood here as a consequence of incomplete character statements and the inappropriate mixing of neomorphic and transformational character statements. Only a few logically complete patterns for morphological character data exist their adoption promises to greatly reduce current variability in character data between analyses.

© The Willi Hennig Society 2007.

“Character” as a cladistic concept was first explored in detail in an influential paper by Patterson (1982 ) entitled “Morphological characters and homology.” Surprisingly, the term “character” was never defined. Patterson used “character” interchangeably with “homolog”, “anatomical singular”, “feature”, and “characteristic” ( Patterson, 1982 , pp. 23, 25). He identified “utilitarian” systematists (e.g., Blackwelder, Crowson, Ross) who equated “character” and “homology”, and Patterson likened this to his view that “homologies are the characters of monophyletic, or natural, taxa” ( Patterson, 1982 , p. 62). For Patterson, characters alone were sufficient to capture morphological transformation following Hennig (1966 , p. 89) and Bock (1974 , p. 387), he suggested that “character” and “character state” are operationally one in the same ( Patterson, 1982 , p. 25). Many authors, perhaps unintentionally, adopt this view when speaking of derived “characters”, rather than derived “character states”—wording that has long been recognized as ambivalent ( Michener and Sokal, 1957 Colless, 1985 Rodrigues, 1986 ).

In contrast to “character”, Patterson (1982 ) presented several definitive statements about “homology.” He developed an idea first forwarded by other cladists that “homology” and “synapomorphy” are best understood as synonyms (e.g., Wiley, 1975 Bonde, 1977 Cracraft, 1978 Nelson, 1978 Nelson and Platnick, 1981 ). Patterson defined “homology” variously as “a hypothesis of monophyletic grouping”, “similarity characterizing monophyletic groups”, a “relation characterizing natural groups”, or simply “discovery” ( Patterson, 1982 , pp. 21, 61, 65), and he differentiated “taxic” from “transformational” homology ( de Pinna, 1991 Rieppel, 1994 ). Others have distinguished “primary homology” (the initial proposition of similarity) from “secondary homology” (shared similarity based on congruence de Pinna, 1991 Brower and Schawaroch, 1996 ). “Character” and “primary homology”, according to these authors, are synonyms (Table 1, definitions 7, 10, 12).

No. Definition Reference
1 “Any attribute of an organism or a group of organisms by which it differs from an organism belonging to a different category or resembles an organism of the same category” Mayr et al. (1953 , p. 315)
2 “those peculiarities that distinguish a semaphoront (or a group of semaphoronts) from other semaphoronts ‘characters’” Hennig (1966 , p. 7)
3 “a theory that two attributes which appear different in some way are nevertheless the same (or homologous)” Platnick (1979 , p. 542)
4 “a part or attribute of an organism that may be described, figured, measured, weighed, counted, scored or otherwise communicated by one biologist to other biologists” Wiley (1981 , p. 8)
5 “we consider a multistate character to be any set of more than two organic or inorganic states that have, through some process, transformed from one into the other” O'Grady and Deets (1987 , p. 268)
6 “attributes of organisms that have undergone evolutionary change…a gene, a morphological trait, an ontogenetic sequence, a behavioral attribute, or any other heritable feature” Mabee (1989 , p. 151)
7 “A primary homology statement is conjectural, based on similarity, and reflects the expectation that there is a correspondence of parts [of organisms] that can be detected by an observed match of similarities” de Pinna (1991 , p. 373)
8 “Any feature that is an observable part of an organism” Grande and Rieppel (1994 , p. 261) Liem et al. (2001 , G-6)
9 “a particular feature interpreted as transformationally homologous to another feature” Zelditch et al. (1995 , p. 180)
10 “(1)…an [sic] hypothesis of primary homology in two or more terminal taxa based on original observations of organisms. (2) A [sic] observable feature of an organism used to distinguish it from another” Kitching et al. (1998 , p. 201)
11 “The terms ‘character’ and ‘primary homology statement’ become one in the same” Williams and Seibert (2000 , p. 185)
12 “any feature shared among organisms that we think will provide information to use in phylogenetic analysis…the sum of features showing particular similarities…topographical homologies…topographical identities…or relationships of primary homology…with each other that we observe in different organisms” Stevens (2000 , p. 82)
13 “hypotheses…subject to the cladistic test of congruence in a parsimony analysis” Forey and Kitching (2000 , p. 55)
14 “an observation that captures distinguishing peculiarities among organisms…a logical relation established between intrinsic attributes of two or more organisms that is rooted in observation and that, if corroborated by congruence, is hypothetically explained as an historical relation” Rieppel and Kearney (2002 , p. 61)
15 “a series of singular historical events” Grant and Kluge (2004 , p. 24)


With 7972 described species grouped in 350 genera, Staphylininae Latreille, 1802 are the third most speciose rove beetle subfamily, after Aleocharinae Fleming, 1821 and Pselaphinae Latreille, 1802 1 . Staphylinine rove beetles are relatively large, fairly robust blunt-headed and short elytra, sometimes colourful, and frequently collected by naturalists. Staphylininae currently encompass seven extant tribes, viz., Arrowinini, Diochini, Maorothiini, Othiini, Platyprosopini, Staphylinini, and Xantholinini. Solodovnikov et al. 2 described an extinct tribe Thayeralinini, representing a stem lineage of Staphylininae and displaying morphological character combinations transitional between extant tribes of Staphylininae and even between Staphylininae and Paederinae. Staphylininae and the closely related Paederinae have been placed in the informal Staphylinine group of subfamilies 1,3 .

A close affinity between Paederinae Fleming, 1821 and Staphylininae is supported by some apomorphies of both adults (metacoxae projecting medially, with posterior margin of metaventrite strongly sinuate and adult protrochantin flat, blade-like, and protruding) and larvae (mandibles without preapical teeth, and abdominal terga and sterna longitudinally divided medially by membranous area) 1 , and by a two-gene-based phylogeny using Bayesian inference 4 . Both subfamilies have long been regarded as distinct and monophyletic groups 1,3,5 . Although there is a lack of a wide phylogenetic analysis of the hyperdiverse Paederinae, the phylogenetic relationships among tribes and key genera of Staphylininae have been extensively explored based on both morphological characters 2,6,7,8,9,10,11 and molecular data 4,12,13,14,15,16 . However, it is quite unexpected that the emerging evidence showed no consensus between the morphology- and molecular-based phylogenetic analyses regarding the relationship between Staphylininae and Paederinae nor the interrelationships among extant tribes of Staphylininae (summarized in Kypke et al. 11 Fig. 1).

Nine proposed topologies between Paederinae and the extant tribes of Staphylininae. Topologies are derived from: T1 (phylogeny based on adult and larval characters, Solodovnikov & Newton 7 ) T2 (phylogeny based on larval characters only, Solodovnikov & Newton 7 ) T3 (first molecular phylogeny of Staphylininae (Bayesian inference) based on four genes Chatzimanolis et al. 12 ) T4 (first molecular phylogeny of Staphylininae (combined parsimony analysis) Chatzimanolis et al. 12 ) T5 (molecular phylogeny based on two genes McKenna et al. 4 ) T6 (molecular phylogeny of Staphylininae based on six genes Brunke et al. 14 ) T7 (molecular phylogeny of Paederinae and some Staphylininae based on five genes Schomann & Solodovnikov 17 ) T8 (molecular phylogeny of Staphylininae based on four genes Zhang & Zhou 16 ) and T9 (parsimonious tree of extant and extinct taxa Kypke et al. 11 ). Note that the subfamily Staphylininae are polyphyletic in T6, T7 and T9.

As proposed in Kypke et al. 11 the hypothesis of a paraphyletic Staphylininae was partly supported in a morphology-based phylogeny by Solodovnikov et al. 2 , in which multiple early Cretaceous staphylinine fossils were analyzed together with extant taxa. Surprisingly, recent molecular phylogenies of Staphylininae based on six genes strongly (Bayesian inference) to moderately (maximum likelihood) rejected both monophyly of Staphylininae, because of a sister group relationship between Platyprosopini (Staphylininae) and Paederinae, and the basal-most position of the ‘Xantholinine-lineage’ of Staphylininae, although that study was principally focused on the tribe Staphylinini 14 . Moreover, the monophyly of Staphylininae was again rejected in another molecular of DNA-based study 17 , although the goal of that study was to assess the position of the paederine genus Hyperomma Fauvel. Recently, Kypke et al. 11 described an extinct genus Vetatrecus with two species from mid-Cretaceous Burmese amber (ca. 99 Ma). Integrated phylogenetic analyses of extant representatives of Staphylininae and Paederinae, as well as the transitional Vetatrecus, demonstrated the first morphology-based evidence for the paraphyly of Staphylininae with respect to Paederinae. The emerging paraphyletic Staphylininae hypothesis based on recent molecular and fossil-integrated morphology-based phylogenies conflicts strongly with the conventional morphological studies of adults and larvae 3,7 and a two-gene based molecular phylogeny 4 .

As with the relationship between Staphylininae and Paederinae, the intertribal relationships of Staphylininae remain elusive, with little work focused primarily on this topic. The first comprehensive phylogenies testing the intertribal relationships of Staphylininae were based on morphological characters, although they were designed to place the New Zealand genus Maorothius Assing (tribe Maorothiini) 6 , or the South Africa genus Arrowinus Bernhauer (tribe Arrowinini) 7 . It is noteworthy that the phylogenetic analyses based on different datasets (adult and larval characters, and larval characters only) in the latter study yielded obviously different topologies, despite the fact that monophyletic Staphylininae were recovered in both analyses. Solodovnikov et al. 2 integrated diverse Cretaceous fossils into the adult morphology-based character matrix from Solodovnikov & Newton 7 , and therefore a very similar topology was produced as expected, and a new extinct tribe Thayeralinini was established. The first molecular phylogeny of the subfamily based on four gene fragments (COI, wingless, topoisomerase I and 28S) was focused on the most diverse tribe Staphylinini, and the tribe Maorothiini was not included 12 . In sharp contrast to the previously published morphology-based phylogeny 7 , the molecular phylogenies using parsimony and Bayesian analyses placed the tribes Othiini and Xantholinini nested within Staphylinini, and Platyprosopini was also recovered as a group within Staphylinini under Bayesian inference. McKenna et al. 4 reconstructed the phylogeny of Staphylinidae and even the series Staphyliniformia and Scarabaeiformia using a new set of DNA sequences, but the relationships above the tribal level were poorly resolved because of limited gene sampling (only two: nuclear 28S rDNA and nuclear protein-coding gene CAD). In particular, the positions of basal staphylinine tribes remained unresolved (Diochini and Platyprosopini) or weakly supported (Arrowinini) under Bayesian inference, and they were completely unresolved under maximum likelihood analysis. Unlike the results in Chatzimanolis et al. 12 , Staphylinini was recovered as a monophyletic group, and Diochini, Othiini and Xantholinini were recovered as isolated lineages sister to Arrowinini + Staphylinini 4 . Brunke et al. 14 provided a more comprehensive molecular phylogeny of Staphylininae based on six genes, which were partially derived from the data first published by Chatzimanolis et al. 12 . Their results rejected the monophyly of Staphylininae and recovered Diochini as sister to other staphylinine tribes and the subfamily Paederinae. Such an unexpected result was further confirmed by Schomann & Solodovnikov 17 , although Staphylininae were represented there by only four extant tribes. In contrast to Brunke et al. 14 , another molecular phylogeny based on four genes by Zhang & Zhou 16 rejected the monophyly of Staphylinini, with Arrowinini nested within it, but the ‘Xantholinini-lineage’ (Diochini, Othiini and Xantholinini) was supported. Recently, the discovery of the Cretaceous genus Vetatrecus (Othiini) and an integrated morphology-based phylogeny combing both extant and extinct taxa further complicated the intertribal relationships of the subfamily Staphylininae 11 .

In this study, we present a novel molecular phylogeny of Staphylininae by mining published DNA data from GenBank. We developed and analyzed a six-gene data set incorporating 92 taxa, including Oxyporinae (outgroup), representatives of Paederinae, and members of all extant tribes of Staphylininae. Additionally, in order to evaluate the congruence between the molecular and morphology-based phylogenies, we re-analyzed the morphology-based (both adult and larval characters) data set from Solodovnikov & Newton 7 and the integrated data set from Kypke et al. 11 using both maximum parsimony and Bayesian inference methods.

Strong morphological support for the molecular evolutionary tree of placental mammals

The emerging molecular evolutionary tree for placental mammals differs greatly from morphological trees, leading to repeated suggestions that morphology is uninformative at this level. This view is here refuted empirically, using an extensive morphological and molecular dataset totalling 17 431 characters. When analysed alone, morphology indeed is highly misleading, contradicting nearly every clade in the preferred tree (obtained from the molecular or the combined data). Widespread homoplasy overrides historical signal. However, when added to the molecular data, morphology surprisingly increases support for most clades in the preferred tree. The homoplasy in the morphology is incongruent with all aspects of the molecular signal, while the historical signal in the morphology is congruent with (and amplifies) the historical signal in the molecular data. Thus, morphology remains relevant in the genomic age, providing vital independent corroboration of the molecular tree of mammals.

Appendix S1 Data matrix in PAUP* format.

Appendix S2 Data matrix in MrBayes format.

Appendix S3 PAUP commands for calculating branch support.

Appendix S4 References for S1–S3.

Figure S1 Strict consensus trees of parsimony analyses of the full taxon set.

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