Outgroup Comparison Method Research Articles

Paropsocolis, a new pentatomid genus with two new species from Brazil (Heteroptera, Pentatomidae, Ochlerini).

When examining specimens of the Janeirona Distant, 1911 clade of Ochlerini (Discocephalinae) we found males and females of two undescribed species. Though clearly similar to the genera in the Janeirona clade, these two species lack the diagnostic characteristics of any of them. We made a cladistic analysis to verify the placement of the two new species in Discocephalinae. A total of 38 taxa and 60 morphological characters were included in the analysis. Character polarization followed the outgroup comparison method, and the most parsimonious trees were calculated in TNT using an implied weighting approach. The analysis resulted in one most parsimonious tree where the two new species form a monophyletic group within the Ochlerini, sister to Janeirona. We propose Paropsocolis Sampaio & Campos, gen. nov. for the two new species Paropsocolis convergens Sampaio & Campos, sp. nov. and Paropsocolis divergens Sampaio & Campos, sp. nov.. The new genus is recognized by having an inconspicuous labial intercalary segment, metasternum anteriorly carinated, parameres with a basal dish-shaped process and a bifurcated apex, theca with one apical ventral process, endosoma with one dorsal and one ventral processes, laterotergites IX surpassing the mediotergite VIII, and thickening of vaginal intima circular. P. convergens Sampaio & Campos, sp. nov. and P. divergens Sampaio & Campos, sp. nov. are described to Brazil. A distributional map is provided.

Cladistics analysis of Calycanthaceae on the basis of morphological and anatomical characters

Cladistics analysis was carried out to find the correct phylogenetic relationship of the four genera of Calycanthaceae. Morphological and anatomical information from all aspect of the data were considered for the analysis. Siparuna guianensis (Siparunaceae) and Cinnamomum malabatrum (Lauraceae) were considered as out-group. Characters were selected mainly for reasonable argument of the similarity. Character-state transformation and discrimination of the genera were decided based upon the out-group comparison method. PAUP* (ver. 4.0) program was used for the dataset analysis and to make phylogenetic tree. The genera split into two separate genera Idiospermum + Chimonanthus and Sinocalycanthus + Calycanthus. Chimonanthus + Idiospermum are supported strict consensus tree with f-value calculation. Furthermore, Sinocalycanthus and Calycanthus are separated genera. Therefore, Calycanthaceae be redefined wide circumscriptions of the characters. The detailed investigation of the cladistics analysis revealed that the Sinocalycanthus and Calycanthus are the sole genus. DOI: http://dx.doi.org/10.5281/zenodo.3908965 Keywords: Calycanthaceae, Characters and characters state, Cladistics, Out-group, Phylogeny

Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions.

Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a “model” of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment. In particular, establishing direction of evolutionary change (character polarization) roots phylogenies and enables testing the existence of historical memory (homology). Unfortunately, rooting phylogenies, especially the “tree of life,” generally follow narratives instead of integrating empirical and theoretical knowledge of retrodictive exploration. This stems mostly from a focus on molecular sequence analysis and uncertainties about rooting methods. Here, we review available rooting criteria, highlighting the need to minimize both ad hoc and auxiliary assumptions, especially argumentative ad hocness. We show that while the outgroup comparison method has been widely adopted, the generality criterion of nesting and additive phylogenetic change embodied in Weston rule offers the most powerful rooting approach. We also propose a change of focus, from phylogenies that describe the evolution of biological systems to those that describe the evolution of parts of those systems. This weakens violation of character independence, helps formalize the generality criterion of rooting, and provides new ways to study the problem of evolution.

Charles Darwin, beetles and phylogenetics

Here, we review Charles Darwin's relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in "The Descent of Man". During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennig's new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data. This has changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics--yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.

Phylogenetic Relationships of Sticklebacks (Gasterosteidae), with Emphasis on Ninespine Sticklebacks (Pungitius SPP.)

Sticklebacks are widely used in comparative biology, but despite past systematic studies, questions of intrarelationships remain. We examined seven nominal species of Pungitius ( P. pungitius , P. occidentalis , P. sinensis , P. tymensis , P. platygaster , P. laevis and P. hellenicus ) and four other species of sticklebacks, Culaea inconstans , Gasterosteus aculeatus , Apeltes quadracus , and Spinachia spinachia , to hypothesize their systematic relationships. Thirty-three informative morphological (osteological and meristic) characters were analyzed. The outgroup comparison method was used for polarizing characters and cladistic methods for reconstructing the systematic relationships of the species. A 50% majority rule consensus tree was calculated for the 32 most parsimonious trees analyzed in the PAUP computer program. The results indicate that S. spinachia is the most primitive member of the family, followed by A. quadracus , and G. aculeatus . It appears that C. inconstans lies within the Pungitius lineage, possibly sister to P. hellenicus , suggesting that C. inconstans should be placed in the genus Pungitius . However, we defer recommending that Culaea be considered a synonym of Pungitius pending further studies to better resolve the Culaea/Pungitius clade.

On the distributional patterns of Southeast‐East Asian freshwater fish and their history

Abstract Aim The extensively published data on Southeast‐East Asian freshwater fish communities and distributions were compiled and expressed into phenograms.Location River basins of Southeast China, the Indochinese Peninsula and Sundaland were studied and compared for possible lineages.Methods The Hennig86 program was employed to cluster the basins of the various subregions on the basis of their similarity in fish assemblages. In this cluster analysis, the outgroup comparison method was used, in which a reference was based on which to make corrections for unequal rates of evolution among the lineages.Results South‐eastern China, the Indochinese Peninsula and Sundaland are groups of landmass that share a common ancestor and that evolved at distinct epochs and through different geological processes, as shown from the association between the distribution of freshwater fish of Southeast‐East Asia and the twenty‐one river basins they inhabit.Main conclusions Southeast‐East Asia comprises an estimated 3500 cyprinid species. The phenograms obtained, based on their compositional and distributional patterns, suggest that the riverine fish communities of the area studied fall into nineteen biogeographical zones defined by the main river systems and their underlying geology.

A cladistic analysis of the Old World species of Lotus L. (Fabaceae: Loteae)

The diagnostic characters of the genus Lotus L. are a claw with a thickened infolded margin, diadelphous stamens, and a style hardened from the base. This genus contains about 100 species that are distributed throughout the world. To investigate the phylogeny of the Old World species of Lotus, subgenus Edentolotus, sections Krokeria, Xantholotus, and Erythrolotus, a cladistic analysis was performed using 31 morphological characters. To test the phylogenetic relationships among species of Lotus-Edentolotus and Dorycnium, Pedrosia, and Tetragonolobus, these taxa were included as part of the ingroup. The polarity of the characters was based on the outgroup comparison method, using Anthyllis as one outgroup and Tripodion as another. The analysis with Anthyllis as outgroup yielded eight equally parsimonious trees (with all characters equally weighted), each with 62 steps, a consistency index of 0.53, and a retention index of 0.75. All trees (including the strict consensus tree from the eight initial trees) showed that genus Lotus, subgenus Edentolotus, and sections Xantholotus and Erythrolotus are polyphyletic, with only section Krokeria appearing as monophyletic. On the other hand, the groups of species Lotus angustissimus, Lotus corniculatus, Lotus creticus, and Lotus peregrinus are monophyletic. Identical results were derived from the data matrix using Tripodion as the outgroup. Results are compared with previous cytogenetic and biochemical evidence.Key words: cladistic analysis, Fabaceae, Loteae, Lotus, Old World species, phylogeny.

Cladistic and Biogeographic Analyses of the Genera Moscharia and Polyachyrus (Asteraceae, Mutisieae)

Abstract The genera Moscharia (two species) and Polyachyrus (seven species) form a monophyletic group within tribe Mutisieae, subtribe Nassauviinae, defined by the leaves with auricles at their bases, and the capitula with 1-seriate involucre. A cladistic analysis of the species of the two genera was carried out using 22 characters from life cycle, external morphology, pollen, and trichomes. Polarity of the characters was based on the outgroup comparison method. One cladogram was produced, with 37 steps, a consistency index of 0.73, and a retention index of 0.75. The cladogram defines six monophyletic groups: (((Polyachyrus annus, (P. carduoides, (P. cinereus, (P. fuscus, P. gayi))), P. sphaerocephalus), P. poeppigii), (Moscharia solbrigii, M. pinnatifida)). The probable ancestral geographic area for the group, determined by Bremer's method, is North- Central Chile area (30°–35° south latitude). The study suggests that the Pleistocene could be the period of evolution of the ancestor of Moscharia and Polya...

Higher Level Phylogeny of Curculionidae (Coleoptera: Curculionoidea) based mainly on Larval Characters, with Special Reference to Broad-Nosed Weevils

A cladistic analysis of Curculionidae was performed using 49 characters (41 from larvae, three from pupae, and five from adults). Illustrations of characters of immatures are provided. The analysis involved 19 terminal units and a hypothetical ancestor determined by the outgroup comparison method used to root the tree. One most parsimonious cladogram was obtained based on the complete data set and the following phylogenetic hypothesis is proposed: Ithycerinae, Microcerinae, and Brachycrinae sensu strictoare broad-nosed weevils placed sequentially at the base of the cladogram. The remaining weevil subfamilies form two major natural groups: one constituted by the sister taxa Rhynchophorinae—Platypodinae; the other with Erirhininae at the base, as sister taxon of the “Curculionidae sensu stricto” which show an unresolved trichotomy involving Curculioninae, Cossoninae—Scolytinae, and the clade including the Entiminae and allied subfamilies. This latter clade of broad-nosed weevils has Thecesterninae at the base; the next branch is Amycterinae, the sister taxon of the clade comprising two groups: one constituted by Aterpinae, Rhytirrhininae, and Gonipterinae; the other is Entiminae whose units form two main clades: one constituted by the sister tribes Pachyrhynchini—Ectemnorhinini, and the other by Alophini, Sitonini, and Entimini. When the analysis was done using only immature characters, results congruent with those based on the complete data set were obtained, except for the placement of Erirhininae. According to the results the hypothesis of monophyly of broad-nosed weevils is not accepted; the Entiminae are justified as monophyletic and their natural classification into tribes is proposed and the phylogenetic position and relationships of higher taxa of Curculionidae are discussed. This paper shows the importance of immature characters in recognition of natural groups and relationships in Curculionidae.

Higher Level Phylogeny of Curculionidae (Coleoptera: Curculionoidea) based mainly on Larval Characters, with Special Reference to Broad‐Nosed Weevils

A cladistic analysis of Curculionidae was performed using 49 characters (41 from larvae, three from pupae, and five from adults). Illustrations of characters of immatures are provided. The analysis involved 19 terminal units and a hypothetical ancestor determined by the outgroup comparison method used to root the tree. One most parsimonious cladogram was obtained based on the complete data set and the following phylogenetic hypothesis is proposed: Ithycerinae, Microcerinae, and Brachycrinae sensu stricto are broad‐nosed weevils placed sequentially at the base of the cladogram. The remaining weevil subfamilies form two major natural groups: one constituted by the sister taxa Rhynchophorinae—Platypodinae; the other with Erirhininae at the base, as sister taxon of the “Curculionidae sensu stricto” which show an unresolved trichotomy involving Curculioninae, Cossoninae—Scolytinae, and the clade including the Entiminae and allied subfamilies. This latter clade of broad‐nosed weevils has Thecesterninae at the base; the next branch is Amycterinae, the sister taxon of the clade comprising two groups: one constituted by Aterpinae, Rhytirrhininae, and Gonipterinae; the other is Entiminae whose units form two main clades: one constituted by the sister tribes Pachyrhynchini—Ectemnorhinini, and the other by Alophini, Sitonini, and Entimini. When the analysis was done using only immature characters, results congruent with those based on the complete data set were obtained, except for the placement of Erirhininae. According to the results the hypothesis of monophyly of broad‐nosed weevils is not accepted; the Entiminae are justified as monophyletic and their natural classification into tribes is proposed and the phylogenetic position and relationships of higher taxa of Curculionidae are discussed. This paper shows the importance of immature characters in recognition of natural groups and relationships in Curculionidae.

A cladistic analysis of the genus Lopezia (Onagraceae)

Lopezia, a genus of 92 species largely restricted to Mexico, forms a monophyletic group defined by the possession of two stamens in tetramerous flowers. A cladistic analysis of the genus was performed using 16 characters from morphology, anatomy and embryology. Twenty of the 22 species were considered the terminal taxa. Polarity of the characters was based on the outgroup comparison method, using three alternative outgroups: the genus Fuchsia , Onagraceae excluding Ludwigia, and Epilobieac-Onagreae. Using Fuchsia as outgroup, 29 equally parsimonious cladograms were produced, each with 24 steps and a consistency index of 0.75. A successive weighting procedure was applied, resulting in 15 cladograms with consistency index of 0.85. The strict consensus cladogram defines eight monophyletic groups and supports most of the current sectional classification of Lopezia, with the exception that no synapomorphy defines section Jehlia. The larger sections Lopezia and Pelozia, although well-defined as clades, are not fully resolved internally. All cladograms support section Riesenbachia as monophyletic. The two alternative hypotheses for outgroups produced similar results: 61 most parsimonious trees, reduced after the successive weighting procedure to 15, which are identical to those produced with Fuchsia as outgroup. These results are discussed in the context of data on cytology and pollination biology.

A cladistic analysis of the genus Lopezia (Onagraceae)

Lopezia, a genus of 92 species largely restricted to Mexico, forms a monophyletic group defined by the possession of two stamens in tetramerous flowers. A cladistic analysis of the genus was performed using 16 characters from morphology, anatomy and embryology. Twenty of the 22 species were considered the terminal taxa. Polarity of the characters was based on the outgroup comparison method, using three alternative outgroups: the genus Fuchsia , Onagraceae excluding Ludwigia, and Epilobieac-Onagreae. Using Fuchsia as outgroup, 29 equally parsimonious cladograms were produced, each with 24 steps and a consistency index of 0.75. A successive weighting procedure was applied, resulting in 15 cladograms with consistency index of 0.85. The strict consensus cladogram defines eight monophyletic groups and supports most of the current sectional classification of Lopezia, with the exception that no synapomorphy defines section Jehlia. The larger sections Lopezia and Pelozia, although well-defined as clades, are not fully resolved internally. All cladograms support section Riesenbachia as monophyletic. The two alternative hypotheses for outgroups produced similar results: 61 most parsimonious trees, reduced after the successive weighting procedure to 15, which are identical to those produced with Fuchsia as outgroup. These results are discussed in the context of data on cytology and pollination biology.

Musculature of the pelvic appendages of the treecreepers (Passeriformes: Certhiidae): myological adaptations for tail-supported climbing

The hind-limb myology of the treecreepers is highly modified compared with the normal passerine pattern, so far as it is known. The muscular modifications involve mainly the iliotibialis cranialis, iliotibialis lateralis, flexor cruris lateralis, pubo-ischiofemoralis, iliotrochantericus medius, iliofemoralis internus, obturatorius lateralis, tibialis cranialis, fibularis longus, plantaris, and some toe flexor muscles. An investigation was carried out into whether the morphological changes in these muscles are related to the specialized mode of locomotion of treecreepers, that is, whether they are adaptations for tail-supported climbing in these species. So far as the principal action of the modified muscles is concerned, it was found that the modifications observed in the hind limb favour flexion of the leg joints or reduce their extension. The adaptative hypothesis is tested using the out-group comparison method on the basis of an available phylogeny.

The Musculi Flexor Perforatus Digiti II and Flexor Digitorum Longus in Paridae

The hindlimb muscles were studied in 17 passerine species. In comparison, Parus spp. showed several myological modifications involving muscles flexor perforatus digiti II and flexor digitorum longus. Considering changes in functional muscular properties these modifications are explained as adaptations of the leg apparatus for an increase in grasping strength in species with a high propensity for hanging upside down under branches. The adaptive hypothesis is tested on the basis of the outgroup comparison method.

A CLADISTIC ANALYSIS OF CIRCAEA (ONAGRACEAE)

Abstract- Circaea (Onagraceae), a genus of seven species from the northern hemisphere, forms a monophylctic group defined by the following synapomorphies: two stamens (opposite the sepals), fruits indehiscent capsules, hooked hairs on the fruits, and perianth parts reduced to two. A cladistic analysis of the genus was performed using 22 characters from morphology, anatomy and palynology. The seven species and seven additional subspecies were considered the terminal taxa. Polarity of the characters is based on the outgroup comparison method. Eighteen equally parsimonious cladograms were produced, each with 32 steps and a consistency index of 0.75. A successive weighting procedure was applied, resulting in six cladograms with a consistency index of 0.95. All 24 cladograms share the following seven monophylctic groups: (1) all species except C. cordala and C. glabrescens (stipules deciduous); (2) the group of C. mollis, the three subspecies of C. lutetiana and C. erubescens (exsertcd nectary); (3) C. repens and all six subspecies of C. alpina (single-seeded fruits, stolons terminated by tubers, and viscin threads reduced or absent); (4) the six subspecies of C. alpina (unilocular ovaries with no trace of a second loculc and tardily opening perianth); (5) C. alpina subspecies alpina, micrantha, pacifica, and imaicola (flowers opening on ascending to erect pedicels); (6) C. alpina subspecies alpina, micrantha, and pacifica (translucent leaves); (7) C. alpina subspecies alpina and murantha (glabrous stems). Results of the cladistic analysis support most of the current systematic classification of the genus, except for the relationships among the three subspecies of C. lutetiana.

A CLADISTIC ANALYSIS OF THE FAMILY TRISTIRIDAE (ORTHOPTERA, ACRIDOIDEA).

Abstract- A cladistic analysis of the endemic South American family Tristiridae was performed using 29 characters from external morphology and the genitalia. Polarity of characters was based on the outgroup comparison method. One most parsimonious cladogram of 54 steps was obtained, from which a classification of the family Tristiridae was constructed. The analysis of phylogenetic relationships showed that the different kinds of characters define taxa at different levels in the cladogram. Those mostly from the phallic complex define suprageneric taxa while those from external morphology characterize genera. It is hypothesized that in Tristiridae differentiation of the phallic complex preceded differentiation of external morphology and that characters from the phallic complex arc less conservative than those from the external morphology.

A Cladistic Analysis of the Genus Cyttaria (Fungi-Ascomycotina).

Abstract-Cyttaria Berkeley (Cyttariaceae, Cyttariales, Class Discomycetes), is a genus of eleven species, seven from South America and four from Australasia (Australia, Tasmania, and New Zealand). Cyttaria is a monophyletic genus defined by the following synapomorphies: fleshy to gelatinous stromata with endostromatic apothecia; and complete lack of fungal chitin in the cell walls, having instead β-1-3-glucan. All Cyttaria are exclusive parasites of Nothofagus species. A cladistic analysis of the genus was performed using 18 characters from macromorphology, micro-morphology, and phenology. Polarity of characters is based on the outgroup comparison method (using the Class Discomycetes as a whole) and on the ontogenetic criterion. A hypothetical outgroup was constructed using all plesiomorphic states. Two equally parsimonious cladograms were produced, each with 40 steps and a consistency index of 0.70. These differed in the position of the South American species C. hookeri and C. johowii. In one cladogram, C. hookeri is the sister group to the rest of the genus, and in the other, both species form a monophyletic group (ascospores ovoid) that is the sister group of the rest of the genus. Our analysis of the two characters causing this difference (position of apothecia on stroma, and shape of ascospores) supports the latter hypothesis. In both cladograms, all of the Australasian species form a monophyletic group (thick ectostroma), and, within that, two subgroups are defined: C. gunnii-C. pallida (papillae present), and C. nigra-C. septentrionalis (ectostroma with black incrustations). The Australasian species form a monophyletic group (spermatangia absent) with C. berteroi, and this last group forms a monophyletic group (conidia absent) with C. espinosae. Cytlaria darwimi and C. exigua form another monophyletic group (very thick ectostroma). Excluding C. hookeri and C. johowii, C. hariotii is the sister group to the remaining eight species.

The Out-Group Comparison Method of Character Analysis

The Out-Group Comparison Method of Character Analysis

The Out-Group Comparison Method of Character Analysis

The out-group comparison method of character analysis. Syst. Zool., 30:1–11.—An operational rule for analyzing character polarity with out-group comparison is presented and a series of observations, including potential problems in applying the rule, are discussed. The “commonality principle” (=“frequency of occurrence,” “common equals primitive”) for determining character polarity is reviewed and dismissed as a reliable alternative to out-group comparison. Based on the rule and observations, a general method for character analysis is synthesized.