Ancestral state estimation and taxon sampling density

A set of experiments based on simulation and analysis found that using the parsimony algorithm for ancestral state estimation can benefit from increased sampling of terminal taxa. Estimation at the base of small clades showed strong sensitivity to tree topology and number of descendent tips. These effects were largely driven by the creation and negation of ambiguity across a topology. Root state and internal state estimation showed similar behavior. We conclude that increased taxon sampling density is generally advisable, and attention to topological effects may be advisable in evaluating the confidence placed in state estimation. We also explore the factors affecting ancestral state estimation and conjecture that as taxa are added to a tree, the total amount of information for root state estimation depends on the tree topology and distance to root state of added taxa. For a pure-birth model tree, we conjecture that the addition of N taxa increases root state information in proportion to log(N).     

Assessing the accuracy of ancestral protein reconstruction methods

The phylogenetic inference of ancestral protein sequences is a powerful technique for the study of molecular evolution, but any conclusions drawn from such studies are only as good as the accuracy of the reconstruction method. Every inference method leads to errors in the ancestral protein sequence, resulting in potentially misleading estimates of the ancestral protein's properties. To assess the accuracy of ancestral protein reconstruction methods, we performed computational population evolution simulations featuring near-neutral evolution under purifying selection, speciation, and divergence using an off-lattice protein model where fitness depends on the ability to be stable in a specified target structure. We were thus able to compare the thermodynamic properties of the true ancestral sequences with the properties of “ancestral sequences” inferred by maximum parsimony, maximum likelihood, and Bayesian methods. Surprisingly, we found that methods such as maximum parsimony and maximum likelihood that reconstruct a “best guess” amino acid at each position overestimate thermostability, while a Bayesian method that sometimes chooses less-probable residues from the posterior probability distribution does not. Maximum likelihood and maximum parsimony apparently tend to eliminate variants at a position that are slightly detrimental to structural stability simply because such detrimental variants are less frequent. Other properties of ancestral proteins might be similarly overestimated. This suggests that ancestral reconstruction studies require greater care to come to credible conclusions regarding functional evolution. Inferred functional patterns that mimic reconstruction bias should be reevaluated.     

No speed dating please! Patterns of social preference in male and female house mice

Glass sponges (Class Hexactinellida) are important components of deep-sea ecosystems and are of interest from geological and materials science perspectives. The reconstruction of their phylogeny with molecular data has only recently begun and shows a better agreement with morphology-based systematics than is typical for other sponge groups, likely because of a greater number of informative morphological characters. However, inconsistencies remain that have far-reaching implications for hypotheses about the evolution of their major skeletal construction types (body plans). Furthermore, less than half of all described extant genera have been sampled for molecular systematics, and several taxa important for understanding skeletal evolution are still missing. Increased taxon sampling for molecular phylogenetics of this group is therefore urgently needed. However, due to their remote habitat and often poorly preserved museum material, sequencing all 126 currently recognized extant genera will be difficult to achieve. Utilizing morphological data to incorporate unsequenced taxa into an integrative systematics framework therefore holds great promise, but it is unclear which methodological approach best suits this task. Here, we increase the taxon sampling of four previously established molecular markers (18S, 28S, and 16S ribosomal DNA, as well as cytochrome oxidase subunit I) by 12 genera, for the first time including representatives of the order Aulocalycoida and the type genus of Dactylocalycidae, taxa that are key to understanding hexactinellid body plan evolution. Phylogenetic analyses suggest that Aulocalycoida is diphyletic and provide further support for the paraphyly of order Hexactinosida; hence these orders are abolished from the Linnean classification. We further assembled morphological character matrices to integrate so far unsequenced genera into phylogenetic analyses in maximum parsimony (MP), maximum likelihood (ML), Bayesian, and morphology-based binning frameworks. We find that of these four approaches, total-evidence analysis using MP gave the most plausible results concerning congruence with existing phylogenetic and taxonomic hypotheses, whereas the other methods, especially ML and binning, performed more poorly. We use our total-evidence phylogeny of all extant glass sponge genera for ancestral state reconstruction of morphological characters in MP and ML frameworks, gaining new insights into the evolution of major hexactinellid body plans and other characters such as different spicule types. Our study demonstrates how a comprehensive, albeit in some parts provisional, phylogeny of a larger taxon can be achieved with an integrative approach utilizing molecular and morphological data, and how this can be used as a basis for understanding phenotypic evolution. The datasets and associated trees presented here are intended as a resource and starting point for future work on glass sponge evolution.     

Relationships among the major lineages of Dictyoptera: the effect of outgroup selection on dictyopteran tree topology

Abstract Dictyoptera, comprising Blattaria, Isoptera, and Mantodea, are diverse in appearance and life history, and are strongly supported as monophyletic. We downloaded COII, 16S, 18S, and 28S sequences of 39 dictyopteran species from GenBank. Ribosomal RNA sequences were aligned manually with reference to secondary structure. We included morphological data (maximum of 175 characters) for 12 of these taxa and for an additional 15 dictyopteran taxa (for which we had only morphological data). We had two datasets, a 59‐taxon dataset with five outgroup taxa, from Phasmatodea (2 taxa), Mantophasmatodea (1 taxon), Embioptera (1 taxon), and Grylloblattodea (1 taxon), and a 62‐taxon dataset with three additional outgroup taxa from Plecoptera (1 taxon), Dermaptera (1 taxon) and Orthoptera (1 taxon). We analysed the combined molecular?morphological dataset using the doublet and MK models in Mr Bayes , and using a parsimony heuristic search in paup . Within the monophyletic Mantodea, Mantoida is recovered as sister to the rest of Mantodea, followed by Chaeteessa; the monophyly of most of the more derived families as defined currently is not supported. We recovered novel phylogenetic hypotheses about the taxa within Blattodea (following Hennig, containing Isoptera). Unique to our study, one Bayesian analysis places Polyphagoidea as sister to all other Dictyoptera; other analyses and/or the addition of certain orthopteran sequences, however, place Polyphagoidea more deeply within Dictyoptera. Isoptera falls within the cockroaches, sister to the genus Cryptocercus. Separate parsimony analyses of independent gene fragments suggest that gene selection is an important factor in tree reconstruction. When we varied the ingroup taxa and/or outgroup taxa, the internal dictyopteran relationships differed in the position of several taxa of interest, including Cryptocercus, Polyphaga, Periplaneta and Supella. This provides further evidence that the choice of both outgroup and ingroup taxa greatly affects tree topology.     

A contribution to sedentary polychaete phylogeny using 18S rRNA sequence data

The phylogenetic position of Annelida as well as its ingroup relationships are a matter of ongoing debate. A molecular phylogenetic study of sedentary polychaete relationships was conducted based on 70 sequences of 18S rRNA, including unpublished sequences of 18 polychaete species. The data set was analysed with maximum parsimony and maximum likelihood methods. Clade robustness was estimated by parsimony-bootstrapping and jackknifing, decay index, and clade support, as well as a posteriori probability tests using Bayesian inference. Irrespective of the applied method, some traditional sedentary polychaete taxa, such as Cirratulidae, Opheliidae, Orbiniidae, Siboglinidae and Spionidae, were recovered by our phylogenetic reconstruction. A close relationship between Orbiniidae and Questa received a particularly strong support. Echiura appears to be a polychaete ingroup taxon which is closely related to Dasybranchus (Capitellidae). As in previous molecular analyses, no support was found for the monophyly of Annelida nor for that of Polychaeta. However, we suggest that an increase in taxon sampling may yield additional resolution in the reconstruction of polychaete ingroup phylogeny, although the difficulties in reconstructing the basal phylogenetic relationships within Annelida may be due to their rapid radiation.     

系统发育分析中的最大简约法及其优化

随着生物技术的不断发展和系统发育学的深入研究, 在重构系统发育树时, 研究人员往往要面对更多的挑战和困难, 比如： (1)需要分析的样本数（物种数或个体数）不断增加; (2)需要分析的数据量迅速扩大。尤其在基因组测序技术的推动下, 基于分子信息的系统发育重建需要极大的计算量, 因此数学方法、 计算机技术以及其他辅助工具对于系统发育重建的效率和精确度起着至关重要的作用。最大简约法（maximum parsimony）是一种重要的系统发育重建方法, 提高其计算效率对系统发育学研究具有重要意义, 针对该算法的优化改进需要生物学家和计算机专家的共同努力。本文通过详细地阐述最大简约法的计算流程, 分析其参数选择对计算效率的影响, 帮助更多的计算机使用者, 在并不了解系统发育学基础的情况下, 更方便地针对实际的系统发育算法问题给出更好、 更快、 更精准的解决方案; 同时为系统发育研究工作者, 较为清晰地解释最大简约法的构树思想和计算逻辑, 推动针对最大简约法的不断改进与优化。     

Reconstructing ancestral ranges in historical biogeography: properties and prospects

Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal--extinction--cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.     

Evolution of habitat preference in Clitellata (Annelida)

Clitellata (earthworms, leeches, and allies) is a clade of segmented annelid worms that comprise more than 5000 species found worldwide in many aquatic and terrestrial habitats. According to current views, the first clitellates were either aquatic (marine or freshwater) or terrestrial. To address this question further, we assessed the phylogenetic relationships among clitellates using parsimony, maximum likelihood and Bayesian analyses of 175 annelid 18S ribosomal DNA sequences. We then defined two ecological characters (Habitat and Aquatic‐environment preferences) and mapped those characters on the trees from the three analyses, using parsimony character‐state reconstruction (i.e. Fitch optimization). We accommodated phylogenetic uncertainty in the character mapping by reconstructing character evolution on all the trees resulting from parsimony and maximum likelihood bootstrap analyses and, in the Bayesian inference, on the trees sampled using the Markov chain Monte Carlo algorithm. Our analyses revealed that an ‘aquatic’ ancestral state for clitellates is a robust result. By using alterations of coding characters and constrained analyses, we also demonstrated that the hypothesis for a terrestrial origin of clitellates is not supported. Our analyses also suggest that the most recent ancestor of clitellates originated from a freshwater environment. However, we stress the importance of adding sequences of some rare marine taxa to more rigorously assess the freshwater origin of Clitellata. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 447–464.     

Phylogenetic trees based on gene content

Comparing gene content between species can be a useful approach for reconstructing phylogenetic trees. In this paper, we derive a maximum-likelihood estimation of evolutionary distance between species under a simple model of gene genesis and gene loss. Using simulated data on a biological tree with 107 taxa (and on a number of randomly generated trees), we compare the accuracy of tree reconstruction using this ML distance measure to an earlier ad hoc distance. We then compare these distance-based approaches to a character-based tree reconstruction method (Dollo parsimony) which seems well suited to the analysis of gene content data. To simplify simulations, we give a formal proof of the well-known 'fact' that the Dollo parsimony score is independent of the choice of root. Our results show a consistent trend, with the character-based method and ML distance measure outperforming the earlier ad hoc distance method. AVAILABILITY: http://www.ab.informatik.uni-tuebingen.de/software/genecontent/welcome_en.html     

Molecular phylogenetics of Fouquieriaceae: evidence from nuclear rDNA ITS studies

Molecular sequence data from the 18S-26S rDNA internal transcribed spacer (ITS) region support the monophyly of Fouquieria sensu lato (Fouquieriaceae) and the three subgenera (subg. Fouquieria, subg. Bronnia, subg. Idria) previously recognized within it. Resolution within subg. Fouquieria differs somewhat between parsimony and maximum likelihood (ML) trees. Section Fouquieria and sect. Ocotilla within subg. Fouquieria are not well supported as monophyletic groups. Uncertainty regarding placement of the root within Fouquieriaceae makes discussion of character evolution within the family difficult. Three root positions are consistent with rate-constant evolution of ITS sequences: (1) along the branch to subg. Idria, (2) along the branch to subg. Bronnia, and (3) along the branch to subg. Fouquieria. The first root position listed is equivalent to an outgroup rooting. The third root position listed is equivalent to a midpoint rooting. Of the three root positions above, only the third is along a branch that may be sufficiently long to act as a long-branch attractor. The first two root positions would result in character reconstruction suggesting that succulent growth forms and white floral pigmentation are ancestral within the family, with shifts to woody growth forms and to red floral pigmentation. The third root position results in equivocal reconstruction of the ancestral growth form, equivocal reconstruction of ancestral floral pigmentation in parsimony trees, and a suggestion of white floral pigmentation as ancestral in ML trees. Two previous hypotheses of polyploid origins are compatible with the molecular data presented here: (1) origin of the tetraploid F. diguetii from F. macdougalii, and (2) allopolyploid origin of the hexaploid F. burragei from the tetraploid F. diguetii and a diploid species similar to F. splendens. Direct descent of the hexaploid F. columnaris from the subg. Bronnia lineage is not supported by our data. An amphiploid origin of F. columnaris involving a member of the subg. Bronnia lineage and an extinct taxon outside subg. Bronnia, however, cannot be ruled out.     

Inferring the ancestral sexuality and reproductive condition in sponges (Porifera)

Considerable diversity abounds among sponges with respect to reproductive and developmental biology. Their ancestral sexual mode (gonochorism vs. hermaphroditism) and reproductive condition (oviparity vs. viviparity) however remain unclear, and these traits appear to have undergone correlated evolution in the phylum. To infer ancestral traits and investigate this putative correlation, we used DNA sequence data from two loci (18S ribosomal RNA and cytochrome c oxidase subunit I) to explore the phylogenetic relationships of 62 sponges whose reproductive traits have been previously documented. Although the inferred tree topologies, using the limited data available, favoured paraphyly of sponges, we also investigated ancestral character‐state reconstruction on a phylogeny with constrained sponge monophyly. Both parsimony‐ and likelihood‐based ancestral state reconstructions indicate that viviparity (brooding) was the likely reproductive mode of the ancestral sponge. Hermaphroditism is favoured over gonochorism as the sexual condition of the sponge ancestor under parsimony, but the reconstruction is ambiguous under likelihood, rendering the ancestry of sexuality unresolved in our study. These results are insensitive to the constraint of sponge monophyly when tracing the reproductive characters using parsimony methods. However, the maximum likelihood analysis of the monophyletic hypothetical tree rendered gonochorism as ancestral for the phylum. A test of trait correlation unambiguously favours the concerted evolution of sexuality and reproductive mode in sponges (hermaphroditism/viviparity, gonochorism/oviparity). Although testing ecological hypotheses for the pattern of sponge reproduction is beyond the scope of our analyses, we postulate that certain physiological constrains might be key causes for the correlation of reproductive characters.     

Efficacy or convenience? Model‐based approaches to phylogeny estimation using morphological data

Model‐based approaches (e.g. maximum likelihood, Bayesian inference) are widely used with molecular data, where they might be more appropriate than maximum parsimony for estimating phylogenies under various models of molecular evolution. Recently, there has been an increase in the application of model‐based approaches with morphological (mainly fossil) data; however, there is some doubt as to the effectiveness of the model of morphological evolution. The input parameters (prior probabilities) for the model are unclear, particularly when concerned with unobserved character states. Despite this, some systematists are suggesting superiority of these model‐based methods over maximum parsimony based on, for example, increased resolution or, in the current study, the preferred phylogenetic placement of an iconic taxon. Here, we revisit a recently published analysis implying such superiority and document the discrepancies between parsimony‐based and model‐based approaches to phylogeny estimation. We find that although some taxa are shifted back to their “traditional” phylogenetic placement, other clades are disturbed. The model‐based phylogenies are better resolved; however, due to the lack of an appropriate model of morphological evolution, the increase in resolving power is probably not meaningful. Similarly, some of the preferred phylogenetic positions of taxa, particularly of labile taxa such as Archaeopteryx, are based solely on analyses employing maximum parsimony as the optimality criterion. Poor resolution and labile taxa indicate a need for further examination of the morphology and not a change in method.     

Reconstructing ancestral character states: a critical reappraisal

Using parsimony to reconstruct ancestral character states on a phylogenetic tree has become a popular method for testing ecological and evolutionary hypotheses. Despite its popularity, the assumptions and uncertainties of reconstructing the ancestral states of a single character have received less attention than the much less challenging endeavor of reconstructing phylogenetic trees from many characters. Recent research suggests that parsimony reconstructions are often sensitive to violations of the almost universal assumption of equal probabilities of gains and losses. In addition, maximum likelihood has been developed as an alternative to parsimony reconstruction, and has also revealed a surprising amount of uncertainty in ancestral reconstructions.     

The evolution and maintenance of delayed implantation in the mustelidae (mammalia: carnivora)

Diapause, the temporary cessation of development at an early life-history stage, is widespread among animals and plants. The range of taxa exhibiting various forms of diapause indicates its enormous ecological significance and highlights its value as a model for examining life-history trait evolution. However, despite the impact of diapause on species ecology, there is little understanding of its adaptive value in many groups. Furthermore, the relative roles of phylogeny and ecology in determining the contemporary expression of the trait remain unresolved. Delayed implantation (DI) is a type of diapause found in several orders of mammals. It is particularly prevalent in the Mustelidae, with mustelids making up more than half of all mammals known to exhibit DI. This taxon is thus ideal for examining life-history predictors of DI and investigating the mode of evolution. Both maximum likelihood and maximum parsimony methods of ancestral state reconstruction indicated DI to be plesiomorphic in the mustelids, although multiple state changes are required to explain its contemporary distribution. After controlling for phylogeny, species with and without DI could be discriminated using just three variables: longevity, maximum latitude of the geographical distribution, and a term describing maternal investment. Our analyses supported the hypothesis that DI is more prevalent in seasonal climates. We also showed that longer-lived species are more likely to exhibit DI, suggesting a time cost to the trait. We found no correlate for the highly variable duration of DI, which remains unexplained. Although ecological factors can predict the distribution of DI in modern mustelids, phylogenetic constraint is likely to play an important role.     

Time-Dependent-Asymmetric-Linear-Parsimonious Ancestral State Reconstruction

The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony. This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated with the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.     

MONOPHYLY OF THE GENUS CLOSTERIUM AND THE ORDER DESMIDIALES (CHAROPHYCEAE, CHLOROPHYTA) INFERRED FROM NUCLEAR SMALL SUBUNIT rDNA DATA

We newly sequenced the nuclear-encoded small subunit (SSU) rDNA coding region for 21 taxa of the genus Closterium. The new sequences were integrated into an alignment with 13 known sequences of conjugating green algae representing six traditional families (i.e. Zygnemataceae, Mesotaeniaceae, Gonatozygaceae, Peniaceae, Closteriaceae, and Desmidiaceae) and five known charophycean sequences as outgroups. Both maximum likelihood and maximum parsimony analyses supported with high bootstrap values one large clade containing all placoderm desmids (Desmidiales). All the Closterium taxa formed one clade with 100% bootstrap support, indicating their monophyly, but not paraphyly, as suggested earlier. As to the taxa within the genus Closterium , we found two clades of morphologically closely related taxa in both maximum likelihood and maximum parsimony trees. They corresponded to the C. calosporum species complex and the C. moniliferum-ehrenbergii species complex. It is of particular interest that the homothallic entity of C. moniliferum v. moniliferum was distinguished from and ancestral to all other entities of the C. moniliferum-ehrenbergii species complex. Superimposing all 50 charophycean sequences on the higher order SSU rRNA structure model of Closterium , we investigated degrees of nucleotide conservation at a given position in the nucleotide sequence. A characteristic "signature" structure to the genus Closterium was found as an additional helix at the tip of V1 region. In addition, eight base deletions at the tip of helix 10 were found to be characteristic of the C. calosporum species complex, C. gracile , C. incurvum , C. pleurodermatum , and C. pusillum v. maius. These taxa formed one clade with an 82% bootstrap value in maximum parsimony analysis.     

Phylogenetics of the woodrat genus Neotoma (Rodentia: Muridae): implications for the evolution of phenotypic variation in male external genitalia

Interspecific morphological variation in animal genitalia has long attracted the attention of evolutionary biologists because of the role genital form may play in the generation and/or maintenance of species boundaries. Here we examine the origin and evolution of genital variation in rodents of the muroid genus Neotoma. We test the hypothesis that a relatively rare genital form has evolved only once in Neotoma. We use four mitochondrial and four nuclear markers to evaluate this hypothesis by establishing a phylogenetic framework in which to examine genital evolution. We find intron seven of the beta-fibrinogen gene to be a highly informative nuclear marker for the levels of differentiation that characterize Neotoma with this locus evolving at a rate slower than cytochrome b but faster than 12S. We estimate phylogenetic relationships within Neotoma using both maximum parsimony and maximum likelihood-based Bayesian methods. Our Bayesian and parsimony reconstructions differ in significant ways, but we show that our parsimony analysis may be influenced by long-branch attraction. Furthermore, our estimate of Neotoma phylogeny remains consistent across various data partitioning strategies in the Bayesian analyses. Using ancestral state reconstruction, we find support for the monophyly of taxa that possess the relatively rare genital form. However, we also find support for the independent evolution of the common genital form and discuss possible underlying developmental shifts that may have contributed to our observed patterns of morphological evolution.     

Molecular phylogenetic relationships and the coevolution of placentotrophy and superfetation in Poecilia (Poeciliidae: Cyprinodontiformes)

Members of Poeciliidae are used as model organisms for experimental studies on natural and sexual selection, and comparative studies of life-history evolution. The latter have demonstrated multiple origins of both superfetation and placentotrophy within Poeciliidae. Most recently, placentotrophy has been described in five species of Poecilia (Pamphorichthys), but only one of these (P.hasemani) shows evidence of superfetation. Here, we use a molecular phylogeny based on concatenated nuclear and mitochondrial gene sequences to test hypotheses of correlated evolution between superfetation and placentotrophy in Poecilia. Taxon sampling included all species in the subgenera Micropoecilia and Pamphorichthys for which the presence or absence of placentotrophy and superfetation have been determined, as well as representatives of all other Poecilia subgenera (Acanthophacelus, Limia, Mollienesia, Poecilia, Pseudolimia). Phylogenetic analyses were performed with maximum parsimony, maximum likelihood, and Bayesian methods; ancestral states for life-history characters were reconstructed with parsimony and SIMMAP; correlation analyses were performed with SIMMAP; and divergence times were estimated using a relaxed molecular clock. All subgenera in Poecilia were recovered as monophyletic. The basal split in Poecilia is between P. (Acanthophacelus)+P. (Micropoecilia) and the other five subgenera. In the latter clade, P. (Poecilia) is the sister-group to the remaining four subgenera. Within P. (Pamphorichthys), all analyses with the combined data set recovered P. (Pamphorichthys) araguaiensis as the sister taxon to P. (Pamphorichthys) hollandi, and P. (Pamphorichthys) scalpridens as the sister taxon to P. (Pamphorichthys) minor. P. (Pamphorichthys) hasemani was either the sister taxon to P. (Pamphorichthys) hollandi+P. (Pamphorichthys) minor (maximum likelihood, Bayesian) or the sister taxon to all other Pamphorichthys species (maximum parsimony). Ancestral state reconstructions suggest that placentotrophy and superfetation evolved on the same branch in P. (Micropoecilia), whereas placentotrophy evolved before superfetation in P. (Pamphorichthys). SIMMAP analyses indicate a statistically significant association between placentotrophy and superfetation. Within P. (Micropoecilia) both placentotrophy and superfetation evolved in ≤4 million years. Within P. (Pamphorichthys), superfetation evolved in ≤9 million years on the P. (Pamphorichthys) hasemani branch, and placentotrophy evolved in ≤10 million years in the common ancestor of this subgenus.     

GROUNDPLANS AND EXEMPLARS: PATHS TO THE TREE OF LIFE

Abstract — During cladistic analysis of a diverse higher taxon it is impractical to code every species as a separate terminal. In such cases, workers proceed in one of two distinct ways: (1) examine a number of member species in order to deduce groundplan character states of the higher group before the analysis is begun, here called the intuitive method, or (2), code a number of real species belonging to the group as terminals in the analysis, called the exemplar method. Both methods have the same aim, to estimate the groundplan of the higher taxon concerned.
Both groundplan estimation methods will lead to identical results when the character in question has the same state in all members of the terminal group, however when the character has two or more states, the two methods may give different results. The precise methods employed in the intuitive approach have not been articulated in the literature, but possible techniques may result in non-parsimonious ancestral state assignments, even in simple cases.
Groundplan estimation in the exemplar method is an extension of parsimony. The exemplar method allows groundplan state/s at internal nodes to be calculated during tree search. In many cases the exemplar method assigns a number of possible states to the groundplan, and the state assignment is therefore equivocal. This is not a deficiency of the method but reflects the notion that the parsimony criterion alone cannot always distinguish a single state present in a hypothetical ancestor. The optimal choice of exemplars required to estimate the groundplan most efficiently is discussed under a simple and common hypothesis of character transformation. For complex character distributions up to three exemplars may be required, each from a separate lineage of the group close to its hypothetical common ancestral node.     

Phylogeny reconstruction using duplicate genes

In this paper, we propose a new method (uninode coding) for coding duplicate (paralogous) genes to infer species trees. Uninode coding incorporates data from duplicated and unduplicated gene copies in phylogenetic analyses of taxa. Uninode coding utilizes global parsimony through the inclusion of both duplicated and unduplicated gene copies, allows one to code all data sources from a taxon into a single terminal, and overcomes problems of character dependence among duplicated and unduplicated gene copies. We present an example of uninode coding using the phytochrome A and phytochrome C data from a study by Donoghue and Mathews.