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Phylogenetic Systematics
... Similarly to phenetics, cladistics emerged in paleontology in the 1960s and gained considerable momentum from the 1970s onward. The seminal German book by Hennig (1950) was largely ignored; it was not until its English translation (Hennig 1966) that cladistics developed. Hennig's (1966) main innovation in phylogenetics was the distinction between the evolutionary significance of primitive and derived states; only the latter suggest close relationships. ...
... The seminal German book by Hennig (1950) was largely ignored; it was not until its English translation (Hennig 1966) that cladistics developed. Hennig's (1966) main innovation in phylogenetics was the distinction between the evolutionary significance of primitive and derived states; only the latter suggest close relationships. Nevertheless, his manual (non-computerized) method for tree searching is no longer used, because homoplasy is arguably more common than what Hennig (1966) expected, and even for relatively small datasets, current phylogenetic software (Swofford 2002;Goloboff and Catalano 2016) are capable of obtaining in seconds much more reliable results than a manual search. ...
... Hennig's (1966) main innovation in phylogenetics was the distinction between the evolutionary significance of primitive and derived states; only the latter suggest close relationships. Nevertheless, his manual (non-computerized) method for tree searching is no longer used, because homoplasy is arguably more common than what Hennig (1966) expected, and even for relatively small datasets, current phylogenetic software (Swofford 2002;Goloboff and Catalano 2016) are capable of obtaining in seconds much more reliable results than a manual search. ...
... Thus "characters" are fundamental data for evolutionary analyses and the character concept is central to evolutionary biology (Wagner, 2000). Initially, comparisons of morphological characters were used in taxonomic classification (Linnaeus, 1758), to study evolutionary processes (Darwin, 1859) and to determine phylogenetic relationships (Hennig, 1965). In principle, a single distinctive character is sufficient to distinguish species and groups of species from one another. ...
... Please insert Figure 2 Here Distinctive characters that define clades are called synapomorphies or shared-derived characters that indicate a monophyletic origin of the character, i.e., synapomorphic characters represent a historically unique origin of an evolutionary novelty in the common ancestor of a clade (Hennig, 1965). Hennig reasoned that only synapomorphies should be used to diagnose common descent by tracing character evolution along a phylogeny. ...
... This seemingly straightforward procedure of character analysis and the algorithmic logic to diagnose clades was developed so that phylogenetic classification is an objective exercise determined by the branching order (Hennig, 1965). ...
The formulation and testing of hypotheses using ‘big biology data’ often lie at the interface of computational biology and structural biology. The Protein Data Bank (PDB), which was established about 50 years ago, catalogs three-dimensional (3D) shapes of organic macromolecules and showcases a structural view of biology. The comparative analysis of the structures of homologs, particularly of proteins, from different species has significantly improved the in-depth analyses of molecular and cell biological questions. In addition, computational tools that were developed to analyze the ‘protein universe’ are providing the means for efficient resolution of longstanding debates in cell and molecular evolution. In celebrating the golden jubilee of the PDB, much has been written about the transformative impact of PDB on a broad range of fields of scientific inquiry and how structural biology transformed the study of the fundamental processes of life. Yet, the transforming influence of PDB on one field of inquiry of fundamental interest—the reconstruction of the distant biological past—has gone almost unnoticed. Here, I discuss the recent advances to highlight how insights and tools of structural biology are bearing on the data required for the empirical resolution of vigorously debated and apparently contradicting hypotheses in evolutionary biology. Specifically, I show that evolutionary characters defined by protein structure are superior compared to conventional sequence characters for reliable, data-driven resolution of competing hypotheses about the origins of the major clades of life and evolutionary relationship among those clades. Since the better quality data unequivocally support two primary domains of life, it is imperative that the primary classification of life be revised accordingly.
... The cladistic analysis combines the morphology, physiology, behavior, ecology, and geographical distribution in order to understand how the species have evolved [4,5] in a temporal framework of evolution. In this kind of study, the extent of resemblance or difference among species is not significant, but the relationships of the characters are inherited from ancestors [4]. ...
... The cladistic analysis combines the morphology, physiology, behavior, ecology, and geographical distribution in order to understand how the species have evolved [4,5] in a temporal framework of evolution. In this kind of study, the extent of resemblance or difference among species is not significant, but the relationships of the characters are inherited from ancestors [4]. ...
... In asteroids, it is the region covering the sides of the arms. 4 The tubular structures with a characteristic shape and a fixed position. 5 Small jawed elements on the body of sea urchins and starfish used to clean the body surface and as defensive means. ...
... XX в. и признавав-XX в. и признавав-в. и признававшей, что классификация может или даже должна отличаться от генеалогии (напр., Bock, 1977), со- Bock, 1977), со-, 1977), современная филогенетическая систематика, основы которой были заложены В. Хеннигом (Hennig, 1966), требует, чтобы система была точным отражением генеалогии (выраженной в иерархии сестринских групп). Наглядной иллюстрацией точки зрения, разделяемой сегодня подавляющим большинством биологов, может служить следующее высказывание Дж. ...
... Однако это не так. Очевидно, что для того, чтобы знать, что признак «наличие лап» является менее общим состоянием признака «наличие конечностей», мы должны иметь представления о трансформационной серии -о чем писал еще Хенниг (Hennig, 1966). Если у нас нет гипотез о трансформационной серии, то как мы узнаем, что плавники превратились в лапы, а не наоборот? ...
... Веским обоснованием неприемлемости парафилетических таксонов служит представление о том, что только монофилетическая группа имеет свою историю и поэтому обладает очевидным преимуществом перед всяческими другими группами (Patterson, 1982). Таким образом, только монофилетические группы представляют собой биологические сущности (естественные группы -Hennig, 1966;Griffiths, 1974;Wiley, 1981;Kitching et al., 1998;Cantino, de �ueiroz, 2010), подлежащие классифициро-�ueiroz, 2010), подлежащие классифициро-�ueiroz, 2010), подлежащие классифициро-, 2010), подлежащие классифицированию. Очевидно, что именно представления о монофилетических группах как природных сущностях, обладающих собственной историей, и обусловили успех филогенетической систематики. ...
Общее признание филогенетической систематики (кладистики) связано с ее кажущей- ся объективностью и адекватностью отражения эволюции в системах, построенных на основании генеалогии. Однако строго монофилетические группы, включающие пред- ставителей различного эволюционного уровня, зачастую не имеют собственной исто- рии, и поэтому кладистическая систематика способствует созданию таксонов со сме- шанной историей, которые не могут считаться естественными объектами. Напротив, парафилетические группы, не приемлемые с позиций кладистики, могут иметь свою собственную эволюционную историю, информация о которой в кладистической си- стеме теряется. Информация о предке не только не заложена в концептуальной основе кладограммы, но и может быть существенно искажена. Поскольку среди ископаемых групп организмов наибольшее распространение имеют парафилетические таксоны, именно палеонтологи, использующие кладистическую методологию, вынуждены чаще всего игнорировать эволюционное содержание биоразнообразия при построе- нии классификаций. В результате этого система перестает служить накоплению зна- ний об эволюции, а ископаемые организмы перестают играть роль в ее познании.
... One century later, Hennig (1966) proposed that not all similarities are equal. And that classifications should reflect the evolutionary history of the group and consequently, only similarities due to common exclusive ancestry should be considered. ...
... Similarities not reflecting this common ancestry, as convergences, should not be used. This methodology, named by Hennig (1966) phylogenetic systematics and later known as cladistics, became quickly the paradigm in biological classification (Schuh and Brower 2009). In the following decades, many classifications were proposed based on this methodology with morphological characters, until molecular characters became increasingly more used in phylogenetic analysis. ...
... Once better understood, these changes were important to understand the past diversity of these groups, potentially identifying recently erected taxa as semaphoronts of previously described species (Horner & Goodwin, 2006;Horner & Goodwin, 2009;Scannella & Horner, 2010;Woodward et al., 2020). Hennig (1966), in his efforts to introduce useful and strictly defined nomenclature to phylogenetic systematics, conceived the "character-bearing semaphoront" as an organism, or individual, at any given point or stage along its ontogeny (Assis, 2016;Rieppel, 2003). Consequently, the definition of term highlights the importance of using corresponding semaphoronts as basis to establish monophyletic groups, as treating different ontogenetic stages as terminals is problematic, especially in paleontology (Sharma et al., 2017). ...
... Yet Xenodontosuchia, here does not exclude Morrinhosuchus luziae Iori & Carvalho, 2009, but does Pakasuchus kapilimai O'Connor et al., 2010 The phylogenetic affinities of Baurusuchidae corroborates previous works, with its main Baurusuchinae/ Pissarrachampsinae dichotomy (Darlim, Montefeltro, & Langer, 2021;Godoy et al., 2018;Montefeltro et al., 2011), with the exception Cynodontosuchus rothi Woodward, 1896, which emerges as a sister to Stratiotosuchus within Baurusuchinae. As previously mentioned, the main objective of the analysis was to codify the juvenile IFSP-VTP/PALEO-0003 in order to observe its systematic placement with respect to adult baurusuchids, testing the degree to which ontogeny affects the topology and the problems with including of juvenile specimens (Hennig, 1966;Sharma et al., 2017). As in Campione et al. (2013), we also sought to compare its placement with G. scabrosus, a putative juvenile and the smallest baurusuchid species known (Marinho et al., 2013). ...
Baurusuchidae comprises a clade of top-tier terrestrial predators and are among the most abundant crocodyliforms found in the Adamantina Formation, Bauru Basin, Brazil (Campanian-Maastrichtian). Here, we provide a detailed description of the cranial and postcranial osteology and myology of the most complete juvenile baurusuchid found to date. Although the preservation of juvenile individuals is somewhat rare, previously reported occurrences of baurusuchid egg clutches, a yearling individual, and larger, but skeletally immature specimens, comprise a unique opportunity to track anatomical changes throughout their ontogenetic series. Its cranial anatomy was resolved with the aid of a three-dimensional model generated by the acquisition of computed tomography data, and its inferred adductor mandibular musculature was compared to that of mature specimens in order to assess possible ontogenetic shifts. A subsequent phylogenetic analysis included the scoring of Gondwanasuchus scabrosus, the smallest baurusuchid species known to date, to evaluate its phylogenetic relations relative to a known juvenile. We find considerable differences between juveniles and adults concerning skull ornamentation and
muscle development, which might indicate ontogenetic niche partitioning, and also anatomical and phylogenetic evidence that G. scabrosus corresponds to a young semaphoront lacking mature cranial features.
... Before going any further, it is worthwhile to mention that the primacy of functional explanations in relation to all other explanations fails because of a lack of a method-ology to discern if a function happens (morphological similarity) due to a common ancestor or only due to common environmental demands. Thus, one must distinguish between homologies (synapomorphies-shared, derived characters) and homoplasies (convergences), and the methodologies for such analysis were developed and are well-known since the last century (Hennig, 1966), that is, it requires a phylogenetic hypothesis in order to distinguish homology from homoplasy. However, as Bock was not committed to this research program, it led him to this kind of difficulty. ...
... The duality of evolutionary explanations is related to two components of character evolution: origin and maintenance 3 . Character origin, and its transformation along history, is a topic covered by the branch of science known as Phylogenetic Systematics; this research program seeks to propose classifications (reflecting the evolutionary process) with a more objective method for the elaboration of a hypothesis of the evolutionary history of groups (ancestral-descendant relation) through a differentiated analysis of the characteristics (homologies) of a set of species including an ancestral (hypothetical) and all its descendants (e.g., Hennig, 1966;Wiley & Libermann, 2011). Character origin is then the result of a phylogenetic tree, in the form of an inference to discern between a character being homolog or homoplasious, in other words, to distingue traits that present separate causes (convergences), from those that result from preserving information from common causes (homologies). ...
Walter Bock was committed to developing a framework for evolutionary biology. Bock repeatedly discussed how evolutionary explanations should be considered within the realm of Hempel's deductive-nomological model of scientific explanations. Explanation in evolution would then consist of functional and evolutionary explanations, and within the latter, an explanation can be of nomological-deductive and historical narrative explanations. Thus, a complete evolutionary explanation should include, first, a deductive functional analysis, and then proceed through no-mological and historical evolutionary explanations. However, I will argue that his views on the deductive proprieties of functional analysis and the deductive-nomo-logical parts of evolution fail because of the nature of evolution, which contains a historical element that the logic of deduction and Hempel's converting law model do not compass. Conversely, Bock's historical approach gives a critical consideration of the historical narrative element of evolutionary explanation, which is fundamental to the methodology of the historical nature of evolutionary theory. Herein, I will expand and discuss a modern view of evolutionary explanations of traits that includes the currentacknowledgement of the differences between experimental and the historical sciences, including the token and type event dichotomy, that mutually illuminate each other in order to give us a well confirmed and coherent hypothesis for evolutionary explanations. Within this framework, I will argue that the duality of evolutionary explanations is related to two components of character evolution: origin, with its evolutionary pathways along with the history, and maintenance, the function (mainly a current function) for the character being selected.
... Willi Hennig (1913Hennig ( -1976 revolutionized phylogenetics by developing cladistics, a rigorous method for reconstructing evolutionary relationships based on shared derived characteristics. His book "Phylogenetic Systematics" laid the groundwork for modern cladistics (Hennig, 1965). Robert H. Whittaker (1920Whittaker ( -1980 proposed the fivekingdom classification system, organizing living organisms into Monera, Protista, Fungi, Plantae, and Animalia. ...
... These trees typically show the relationships in a hierarchical manner, with branches splitting into two or more lineages, representing speciation events or divergence points. The concept of "phylogenetic relationship" states that species B is more closely related to species C than to species A if B and C share at least one common ancestral source that is not shared with species A (Figure 1; Hennig, 1965). A phylogenetic tree consists of nodes, branches, and tips or nodes and illustrate the evolutionary connections between different taxa -day taxa being analyzed (see organisms that share a common ancestor and all its descendants, two taxa that share a common ancestor not shared by any other taxa in may represent genetic or evolutionary distances, indicating the amount of change or time elapsed between taxa. ...
... The correlation between species diversification and key innovations, as well as the impact of clade age --older clades should be more diverse on average than younger clade--on the species richness (Scholl & Wiens, 2016), have been examined using different methods (Ree, 2005;Pagel & Meade, 2006;Freckleton et al., 2008;Adams et al., 2009;Vamosi & Vamosi, 2010;Rabosky, 2017). Nevertheless, this relationship has not been investigated using phylogeny-based approaches, particularly those that incorporate holomorphology, which is the totality of characters, as a proxy for evolutionary descent (sensu Hennig, 1966). In addition, the evaluation of morphological synapomorphies within a formal cladistic framework, accompanied by tests of congruence for morphological characters, potentially provides a more accurate approach to identifying putative "key innovations" (Rohde, 1996;Assis & de Carvalho, 2010), compared to solely mapping morphological characters of interest onto the molecular tree (De Pinna, 1991;Assis & de Carvalho, 2010). ...
... Secondly, we perform phylogenetic analyses to examine the relationship between species diversification and putative key innovations (supported by homology assessments). We use the concatenation of data to delimit morphological synapomorphies, inferred with the support of the congruence test, which is a clear and testable criterion (Hennig, 1966;Assis & Carvalho, 2010), to discuss putative key morphological innovations in a broad sense.Furthermore, based on the assumption that species richness may be a better estimate for clade diversity than diversification rates (Rabosky, 2009), we discuss the patterns of total diversification, as well as the impact of age on the diversification of the species-rich genera in Brazil. Accordingly, we aimed to answer the following questions: (i) Does a greater number of taxa within an order coincide with a greater number of key innovations? ...
The disparity in species richness among clades of angiosperms is partly explained by differences in evolutionary and biogeographic processes; however, part of this imbalance remains elusive. The relationships between species diversification
and key innovations, as well as the impact of clade age, are also predicted to explain such disparities. This relationship has not been examined using phylogeny-based approaches based on holomorphology, i.e., concatenated morphological
and molecular datasets. Despite some large-scale evolutionary studies that have contributed to the knowledge of Brazilian flora, the evolutionary history of angiosperms endemic to Brazilian provinces has not yet been elucidated. Therefore, this study had two principal targets. First, we investigated the species richness and distribution patterns of endemic angiosperm genera. Secondly, we perform a phylogenetic analysis based on holomorphology to examine the relationship between species diversification and putative key innovations (by homology assessments) and the effects of clade age on diversification in species-rich genera. We identified the occurrence of 341 exclusive genera (45% monotypic) in 61 families. Our results indicate a positive correlation between diversification and the number of putative key innovations per order but a negative or non-existent one per family. Furthermore, our findings contradict the idea that clade age is associated with species-rich genera, challenging the notion that clade age is a determining factor in species richness. The results showed that 14 traits are closely associated with diversification, and the confluence between biotic and abiotic factors drove the diversification of species-rich genera in the Atlantic Forest, Caatinga, Cerrado, and Parana provinces.
... Biological classifications should be based on phylogenetic reconstruction, which is the best way: (1) to understand how all characters found in one lineage have evolved; and (2) to highlight the characters that should be used for group recognition (e.g., Wiley & Lieberman, 2011). Hennig (1966) argued that groups of organisms at all taxonomic levels should only be delimited based on morphological synapomorphies. However, the utilization of molecular data in phylogenetic studies since the early 1990s has revolutionized the understanding of macroevolution and relationships among organisms, and classifications are often updated accordingly (e.g., Cantino & al., 2007;APG IV, 2016;PPG I, 2016). ...
The use of molecular data in phylogenetic reconstruction during more than three decades has greatly improved our understanding of the macroevolutionary history of the coffee family (Rubiaceae) and has provided a solid basis for improvement of its classification. Based on the results of 130 studies, among them most recent phylogenomic works, we present a consensus phylogeny and a robust classification of Rubiaceae that shed light on the evolutionary success of this highly diverse angiosperm family and can serve as a framework for ecological and evolutionary studies. There are more than 14,000 species and about 580 accepted genera of Rubiaceae that are assigned to 71 tribes, of which 68 are classified in two subfamilies (Dialypetalanthoideae with 38 tribes and Rubioideae with 30 tribes). Three tribes (Acranthereae, Coptosapelteae, Luculieae) remain unclassified as to subfamily. Sixty‐three of these 71 tribes are assigned to nine informal alliances (four in Rubioideae and five in Dialypetalanthoideae). These tribes are listed in alphabetical order within their respective alliances. Five tribes, one (Coussareeae) in Rubioideae and four (Airospermeae, Jackieae, Retiniphylleae, Steenisieae) in Dialypetalanthoideae, are excluded from these alliances due to unclear or conflicting phylogenetic positions. Thirty‐six tribes retain their tribal status but receive new generic limits to remedy their previous para‐ or polyphyletic nature. Twenty‐nine tribes not implemented in previous classifications have been added, of which three (Chioneae, Glionnetieae, Temnopterygeae) are newly described here. Basic information on phylogenies, distributions, former classifications, and useful references to previous works are provided for all accepted tribes, and future perspectives are discussed.
... From a purely cladistic approach, the species in a monophyletic group are contained in a clade that shares a hypothetical common ancestor (Hennig, 1999). However, the Hennigian perspective has been criticized for its unrealistic and biased view of the complexities in the evolutionary transformations of organisms, and especially for denying the real existence of ancestors (Cavalier-Smith, 2010;Mayr, 1973). ...
Ecological and geographical factors shape the current distribution of species. Analysing their interplay in a phylogenetic framework is key to understand the historical processes that have shaped the evolution of a group. Here, we modelled the ecological niches and geographic distributions of the five species of doraditos ( Pseudocolopteryx spp.) to study their biogeographic histories, niche evolution and speciation process in a phylogenetic framework. Our potential distribution models uncovered novel range‐wide distributional patterns and seasonal movements in the doraditos, where four species are migratory with distinct breeding and non‐breeding distributions, and one ( P. sclateri ) exhibits a complex spatiotemporal distribution indicating nomadism. Ecological niche pairwise comparisons showed that none of the doraditos have equivalent niches and that niche differences are due to species‐specific habitat preferences. Phylogenetically weighted geographical and ecological analyses showed patterns of allopatric speciation and niche lability in the evolution of doraditos. The divergence of P. sclateri seems tied to its tropical‐to‐temperate wetland specialization. The montane P. acutipennis expanded to human‐modified lowlands following speciation, highlighting the need to control for post‐speciational changes in ecological niche comparisons as done here. In turn, P. dinelliana , P. citreola and P. flaviventris showed essentially allopatric breeding distributions, as a product of environmentally mediated divergence during their speciation processes. The distribution and migration data of the recently diverged cryptic sister species P. citreola and P. flaviventris are consistent with two possible speciation scenarios: peripatric speciation and migration dosing speciation.
... To conclude on this point of reflection between interpretation and discussion on processes and taxonomy in the context of a phylogenetic analysis, let us recall that Tassy (1991) specifies that if the concept of phylogeny is conceived as the history of ruptures in the gene "pools" and the appearance of new "pools" isolated between populations, then we should indeed speak of tokogeny (Wheeler and Meier, 2000). This term describes infraspecific relationships according to Hennig (1966), who adds that relationships between terminal taxa are not necessarily hierarchical. Thus, if the aim of phylogeny is to put forward hypotheses of relationships between units seen as recognisable, isolated and closed sets, these units may be species but not necessarily identical to the evolutionary units. ...
... Tschulok (1922: 195) consequently reduced phylogeny reconstruction from the search of "direct ancestors" to the specification of "possible ancestors. " Willi Hennig (1913Hennig ( -1976, the acclaimed "founder" of phylogenetic systematics, went beyond Tschulok with his claim that the search for ancestors and descendants should be abandoned altogether, and replaced with a search for sister-group relationships on the basis of shared derived characters (Hennig, 1950(Hennig, , 1965(Hennig, , 1966: "Heterobathmy is therefore a precondition for the establishment of the phylogenetic relationships of species and hence a phylogenetic system" (Hennig, 1965: 107). Species A is more closely related to species B than either is to species C if the sister species A and B share a hypothetical common ancestral species that is not also ancestral to C. These relationships can be hypothesized if it can be shown that A and B share one or several derived character(s) that is/ are not also shared by C. ...
The modern discussion of living fossils turns mostly on the persistence of archaic, or ancestral, traits in extant organisms. Prime examples mentioned by Darwin already—who also coined the term “living fossil”—include the platypus and the extant lungfishes. However, the identification of archaic traits in extant organisms requires a basis of comparison, i.e., it requires an estimate of the phylogenetic interrelationships of the living fossil in question. Phylogenetic relationships are determined not on the basis of the persistence of archaic traits, but on the basis of shared derived characters. The identification of persistent traits in an organism requires the same organism to also exhibit advanced, or specialized traits that allow its proper classification. The occurrence of such a mixture of primitive (plesiomorphic) or derived (apomorphic) traits in an organism, or species, is called the heterobathmy of characters. Willi Hennig recognized the heterobathmy of characters as quite a universal phenomenon, and made it the basis of his phylogenetic systematics.
... Numerical taxonomy introduced a series of quantitative methods to eliminate influences from intuitive judgements and allow studies to be reproducible. Along the same lines, Hennig (1966) launched the study of cladistics at almost the same time. While both phenetics and cladistics use morphological characters as input data, the former clusters taxa based on overall morphological similarity while the latter clusters taxa based on evolutionary relationships (i.e., inferring monophyletic clades using synapomorphies, or shared derived character states). ...
The accumulation of large datasets and increasing data availability have led to the emergence of data-driven paleontological studies, which reveal an unprecedented picture of evolutionary history. However, the fast-growing quantity and complication of data modalities make data processing laborious and inconsistent, while also lacking clear benchmarks to evaluate data collection and generation, and the performances of different methods on similar tasks. Recently, artificial intelligence (AI) has become widely practiced across scientific disciplines, but not so much to date in paleontology where traditionally manual workflows have been more usual. In this study, we review >70 paleontological AI studies since the 1980s, covering major tasks including micro-and macrofossil classification, image segmentation, and prediction. These studies feature a wide range of techniques such as Knowledge-Based Systems (KBS), neural networks, transfer learning, and many other machine learning methods to automate a variety of paleontological research workflows. Here, we discuss their methods, datasets, and performance and compare them with more conventional AI studies. We attribute the recent increase in paleontological AI studies most to the lowering of the entry bar in training and deployment of AI models rather than innovations in fossil data compilation and methods. We also present recently developed AI implementations such as diffusion model content generation and Large Language Models (LLMs) that may interface with paleontological research in the future. Even though AI has not yet been a significant part of the paleontologist's toolkit, successful implementation of AI is growing and shows promise for paradigm-transformative effects on paleontological research in the years to come.
... Another type of phylogenetic analysis, cladistics, compares characters in related taxa to determine relationships between ancestors and descendants. It is a specific method that assumes a relationship between taxa [27]. Cladistics focuses on inferring evolution from changes in individual features (characters in the biological sense) or changes in feature states (character states in the biological sense). ...
This paper introduces the concept of pattern systems that evolve, with a focus on scripts, a specific type of pattern system. The study analyses the development of different script systems, known as scriptinformatics, with a focus on the historical Rovash scripts used in the Eurasian steppe. The aim is to assess the traditional classification of historical inscriptions, referred to as script relics, into distinct Rovash scripts. Clustering and ordination techniques were used to perform multivariate analyses on Rovash scripts and inscriptions. The study presents two new measures, the script-specific holophyletic index and the joint holophyletic index, for evaluating trees produced by hierarchical clustering. The results indicate that holophyletic indices can validate the traditional assignment of inscriptions to scripts through phylogenetic tree evaluation. This method can be extended to include pattern systems with evolutionary properties and graph sequences derived from them, as well as additional scripts and inscriptions.
... Discovery and description of new species since the time of Linnaeus and Pallas, were based on the individual experience of the naturalists. Longlasting discussions were going in attempts to identify the most informative phenotypic characters that could help to separate "real" species from less meaningful traits that could vary among conspecific populations or morphs or make taxonomy more objective by introducing numerical analysis [2][3][4][5][6][7][8][9]. By the XX century, a generation of taxonomists arose, specialized on smaller organismal groups, such as individual families of beetles or butterflies. ...
Despite the increasing deficit of taxonomic expertise, the number of newly described species since the early 2010s has grown exponentially. This growth is related to the increased use of DNA markers in taxonomic descriptions. However, routine use of DNA markers in taxonomy did not bring practical taxonomy closer to the theory. Species are unique lineages with irreversible evolutionary pathways, and only the presence of distinct populations within the same geographic range, or at least the presence of narrow hybrid zones between the parapatric ranges is a conclusive evidence of evolutionary irreversibility. In the case of allopatric populations, only very high genetic distances, suggesting several tens of millions of years of independent evolution, can be used for validation of species status. This problem cannot be solved by the broader introduction of genomic phylogenies, which also fail to provide robust criteria for evolutionary irreversibility. We can hardly suppose that robust validation of species status is applicable to all or most of hundreds of thousands of animal species, including 20,000 amphibians and reptiles. Instead, practical taxonomy should concentrate on describing recognizable species, maintaining a trade-off between sufficiently detailed descriptions of world biodiversity and the applicability of these descriptions for practical use and metaanalyses, not pretending that formally described species reflect real lineages with independent and irreversible evolutionary pathways. Simultaneously, the non-critical elevation of the taxonomic status of individual geographic populations, contrary to the declared purpose of better-focusing conservation efforts, often has the opposite effect, leaving many formally described taxa outside the conservation umbrella.
... Systematists generally agree that genus-rank categories should be composed of monophyletic groups of species, and this is a central tenet of the synapomorphy-based system of classification (Hennig 1965, Dubois 1982, Stevens 1985. However, there is often disagreement about how inclusive such groups should be and what criteria should be applied to determine generic limits. ...
Hawks, eagles, and their relatives (Accipitriformes: Accipitridae) are a diverse and charismatic clade of modern birds, with many members that are instantly recognized by the general public. However, surprisingly little is known about the relationships among genera within Accipitridae, and several studies have suggested that some genera (in particular, the megadiverse genus Accipiter) are not monophyletic. Here, we combine a large new dataset obtained from ultraconserved elements, generated from whole genome sequencing of 134 species, with publicly available legacy markers (i.e. a suite of commonly sequenced mitochondrial and nuclear genes) to infer a well-supported, time-calibrated phylogeny of 237 extant or recently extinct species. Our densely sampled phylogeny, which includes 90% of recognized species, confirms the non-monophyly of Accipiter and provides a sufficient basis to revise the genus-level taxonomy, such that all genera in Accipitridae represent monophyletic groups.
... shared, derived characters) are scarce. Only the latter can be used to determine phylogenetic relationships, i.e. taxa sharing an immediate common ancestor (Hennig 1966;Wiley 1979). ...
We examined the morphological characters and internal anatomical features of the electric ray genus Diplobatis (Torpediniformes, Narcinidae) in order to determine the taxonomic status of the various forms. All specimens from the northern coast of South America (Colombia to Brazil) were found to be very variable in most morphological characteristics but to be identical in skeletal structure. Based on overlapping proportional measurements and a lack of distinguishing characters (both internal and external), D. altenai Boeseman 1963 is synonymized with D. pictus Palmer 1950, and the placement of D. guamachensis Martin 1957 in synonymy with D. pictus by Bigelow and Schroeder (1962) is verified. Three subspecies are recognized within D. pictus: D. pictus pictus Palmer, D. pictus guamachensis Martin, and D. pictus colombiensis new subspecies. D. ommata (Jordan and Gilbert 1890), from the Pacific coasts of Mexico and Central America, is found to be identical to D. pictus in skeletal anatomy and similar to its congener in most proportional measurements. D. ommata is distinguished from D. pictus by its dorsal color pattern and differing clasper morphology. The genus and species of Diplobatis are redefined, and the three subspecies are described. Finally, the four genera of Narcinidae (Benthobatis, Diplobatis, Discopyge, and Narcine) are compared and found to be very conservative anatomically. A phylogenetic analysis based on synapomorphic character states shows Discopyge and Narcine to be the sister group to the other narcinids.
... Considering the whole span of arthropod life, the German entomologist Willi Hennig popularized (if briefly) the 'semaphoront' concept, defined by him as an organism at a particular time in its life history, from conception to death (Hennig, 1965). A species constitutes a collection of more or less distinct semaphoronts, where all of them are essential aspects of its biology. ...
Synthetic studies of arthropod systematics and biodiversity are hindered by overreliance on ‘preferred’ semaphoronts, those life stages (typically adult males) that provide the most taxonomically distinctive characters. However, modern sequence-based methods for inventory have no such limitations and permit incorporation of any and all representatives of a species. Here, we briefly review the growth and potential of these approaches to faunistic and systematic studies and share results from our own recent work that illustrate the value that other morphs, immature stages and females added to these studies.
... Of course, "monophyletic groups" (clades) are not lineages, lineages are not clades, and tokogenetic relationships are not phylogenetic relationships. Furthermore, lineages are not dimensionless unitary lines through time (despite the etymological connotation), but rather are populations of organisms reproducing themselves generation over generation, and if they are sexual, interbreeding to produce tokogenetically distinct offspring (Hennig, 1966;Brower, 2021). Thus, if we want to talk about fundamental units that have processual agency, we need to talk about organisms, or perhaps populations, not "lineages". ...
... We propose nine transformation series (Hennig 1966;Grant and Kluge 2004) to account for the variation of the buccopharyngeal morphology in the larvae of Atelopus in comparison with other bufonids. The character matrix was built and edited in Mesquite V. 3.70 (Maddison and Maddison 2021) (Supporting Information), and character optimization was performed in T.N.T. v. 1.5 (Goloboff and Catalano 2016). ...
The Neotropical genus Atelopus is the most diverse genus of bufonids comprising 99 species. Tadpoles of these frogs are
readily distinguished based on the presence of a belly sucker, used by them to stay attached to rocks in fast-flowing streams.
Despite their intriguing biology, information about their anatomy is scarce and many morphological systems are unknown.
We describe the buccopharyngeal cavity of five Atelopus species. The Atelopus buccopharyngeal cavity is characterized by
(1) presence of a pendulum-like papillae in the prenarial arena, (2) presence of a glandular zone in the prenarial arena, (3)
narial vacuities, (4) conical median ridge, (5) absence of buccal roof arena papillae, (6) absence of buccal roof pustulations,
(7) single pair of infralabial papillae, (8) absence of lingual papillae, and (9) absence of pustulations in the buccal floor. We
propose that characters 1, 2, and 3 are new synapomorphies for the genus. We also propose that the presence of a single pair
of infralabial papillae is a synapomorphy for bufonid. Finally, we discuss the convergent evolution of gastromyzophorous
and suctorial tadpoles withing anurans.
... Discrete and Meristic Traits 714 Morphological traits underpin the study of phenotypic evolution within phylogenetic systematics 715 (Hennig, 1966 Mitteroecker and Schaefer, 2022). Raw coordinates are then transformed using a 780 superimposition method, commonly Procrustes analysis, which uses scaling, rotation and 781 transformation to register objects to a common reference frame so that only biological variation 782 remains (Bookstein, 1997). ...
Artificial intelligence (AI) is poised to transform many aspects of society, and the study of evolutionary morphology is no exception. Machine learning-grade methods of AI such as Principal Component Analysis (PCA) and Cluster Analysis have been commonplace in evolutionary morphology for decades, but the last decade has seen increasing application of Deep Learning to ecology and evolutionary biology, opening up the potential to circumvent longstanding barriers to rapid, big data analysis of phenotype. Here we review the current state of AI methods available for the study of evolutionary morphology and discuss the prospectus for near-term advances in specific subfields of this research area, including the potential of new AI methods that have not yet been applied to the study of morphological evolution. We introduce the main available AI techniques, categorising them into three stages based on their order of appearance: (i) Machine Learning, (ii) Deep Learning with neural networks and (iii) the most recent advancements in large-scale models and multimodal learning. Next, we present existing AI approaches and case studies using AI for evolutionary morphology, including image capture and segmentation, feature recognition, morphometrics, phylogenetics, and biomechanics. Finally, we discuss areas where there is potential, but no current application of AI to key areas in evolutionary morphology. Combined, these advancements and potential developments have the capacity to transform the evolutionary analysis of organismal phenotype into evolutionary phenomics, launch it fully in the “Big Data'' sphere, and align it with genomics and other areas of bioinformatics.
... Cladistics is an evolutionary approach usually associated with the application of parsimony to infer relationships among species by analyzing homologous characters and identifying derived shared states to establish monophyletic groups (J. S. Farris, 1983;J. S. Farris et al., 1970;Hennig, 1966). It requires that characters are ontologically independent entities and variation is discretized into mutually exclusive states (J. S. Farris, 1983; J. S. Farris et al., 1970;Sereno, 2007). ...
Quantitative traits are a source of evolutionary information often difficult to handle in cladistics. Tools exist to analyze this kind of data without subjective discretization, avoiding biases in the delimitation of categorical states. Nonetheless, the ability of continuous characters to accurately infer relationships is incompletely understood, particularly under parsimony analysis. This study evaluates the accuracy of phylogenetic reconstructions from simulated matrices of continuous characters evolving under alternative evolutionary processes and analyzed by parsimony. We generated 100 trees to simulate 9,000 matrices containing 26 terminals and 100 continuous characters evolving under: Brownian-Motion (BM), Ornstein-Uhlenbeck (OU) and Early-Burst (EB) processes assuming variable parametrizations. Our comparisons of cladograms revealed that matrices analyzed by parsimony carry phylogenetic signals to infer relationships, but the accuracy is higher for matrices simulated under BM, regardless of the parameterization schemes. Implementation of equal or implied weighting with multiple penalization strengths against homoplasies did not affect cladogram inferences. Accuracy of continuous characters in resolving relationships is skewed toward apical nodes of the trees. Our simulations provide controlled tests of the usefulness of quantitative traits in phylogenetics, specifically under neutral evolution, and demonstrate their effectiveness in estimating shallower nodes among recently diverged species, regardless of parameters and weighting schemes.
... Charles Darwin posited speciation as a gradual process in On the Origin of Species (Darwin, 1859) but did not fully engage with the question of what makes a species a species, nor fully describe the mechanisms that underpin their evolution. Ernst Mayr in 1942 was the first to discuss the question of what a species is, proposing the Biological Species Concept (BSC) (Mayr, 1942); since then many other species concepts have been introduced: Phylogenetic Species Concept (PSC) (Ghiselin, 1974;Pigliucci, 2003), Evolutionary Species Concept (ESC) (Hennig, 1966;Simpson, 1951), and so on. ...
Molecular data has become a powerful tool for species delimitation, particularly among those that present limited morphological differences; while the mitochondrial genome, with its moderate length, low cost of sequencing and fast lineage sorting, has emerged as a practical data set. Due to the limited morphological differences among the closely related species of Carbula Stål 1865, the species boundaries between Carbula abbreviata (Motschulsky, 1866), Carbula humerigera (Uhler, 1860), and Carbula putoni (Jakovlev, 1876) have remained particularly unclear. In this study, we applied two phylogenetic reconstruction methods to two data sets (mitogenome and COI) to assess the phylogeny of Carbula distributed in Asia, and five species delimitation methods to determine the boundaries between East Asian Carbula species. Our phylogenetic analyses showed Carbula to be paraphyletic; the seven known species distributed within East Asia to form a single monophyletic group, and within this, C. abbreviata, C. humerigera, C. putoni and middle-type to comprise a C. humerigera species complex. Our results show that mitogenome data alone, while effective in the differentiation of more distantly related Carbula species, is not sufficient to accurately delimit the species within this newly described complex. Arch Insect Biochem Physiol. 2023;115:e22075. wileyonlinelibrary.com/journal/arch
... After mapping characters onto a phylogeny, ETs can be singled out as chains of states from ancestral nodes to tips. Similar concepts to ETs have been previously explored, such as character phylogeny, transformation series (Hennig, 1966), or character state trees (Farris, 1970). Ultimately, the main focus lies in constructing hypotheses regarding transitions between characters along an ET (Michevich, 1982). ...
Evolutionary tempo and mode summarize ancient and controversial subjects of theoretical biology such as gradualism, convergence, contingence, trends, and entrenchment. We employed an integrative methodological approach to explore the evolutionary tempo and mode of Lepidosaurian Phalangeal Formulae (PFs). This approach involves quantifying the frequencies of morphological changes along an evolutionary trajectory (ET). The five meristic characters encoded by PFs are particularly valuable in revealing evolutionary patterns, owing to their discrete nature and extensive documentation in the literature. Based on a pre-existing dataset of PFs from 649 taxa (35 Lepidosauria families, including fossils), from which there exists a unique repertoire of 53 formulations, our approach simultaneously considers phenetic and phylogenetic data. This culminates in a diagram accounting for the phylogenetic dynamic of evolution traversing across different regions of morphospace. The method involves enumerating phenotypical options, reconstructing phenotypes across the phylogeny, projecting phenotypes onto a morphospace, and constructing a flow network from the frequency of evolutionary transitions between unique phenotypic conditions. This approach links Markovian chains and evolutionary trajectories to formally define parameters that describe the underlying transitions of morphological change. Among other results, we found that: (i) PF evolution exhibits a clear trend toward reduction in the phalangeal count, and that (ii) evolutionary change tends to occur significantly between morphologically similar PFs. Notwithstanding, although minor but not trivial, transitions between distant formulas -jumps- occur. Our results support a pluralistic view including stasis, gradualism, and saltationism discriminating their prevalence in a target character evolution.
... By the 1950s, phylogenetic branching patterns were explicitly discussed across many assemblages of parasites and hosts, including tetrabothriids, and a continuum from higher taxa to species relationships (e.g., Baer, 1954;Mayr, 1957;Szidat,1964). Only later in 1979 was a robust methodology available to develop insights about parasite phylogeny (Hennig, 1966;Brooks, 1979). Subsequently, explicit and direct comparisons became possible for exploring tree topology, evolutionary connectivity, and biogeography among assemblages of parasites and hosts (Brooks, 1981;reviewed in Brooks and McLennan, 2002;Brooks et al., 2019;Trivellone and Pannasiti, 2022). ...
In the biosphere, limits for diversity among species, communities, and biomes are revealed through intensive and extensive field-based inventory and assembly of voucher specimens and associated informatics examined in a phylogenetic, historical, ecological, and biogeographic arena. Archival resources for specimens and information contribute to a cumulative view of faunal structure and assembly under a comparative umbrella. Ultimately, species definitions, and inclusive partitions among populations and lineages, are fundamental in articulating hypotheses that examine interactions about evolution, the nature of organisms, and the condition of environments across space and time. We conclude our proposals establishing species limits for tapeworms of the cryptic complex historically accommodated in Tetrabothrius jagerskioeldi Nybelin, 1916 among Alcidae seabirds (Charadriiformes). Explorations of this facet of marine diversity summarize inventory data for species of Tetrabothrius Rudolphi, 1819 from field collections among 1,976 seabirds of 41 species representing 3 avian orders (Charadriiformes, Suliformes, Procellariiformes) examined across 58 oceanic/geographic localities from the greater North Pacific basin between 1949 and 2019, or over the past 70 years. Cestodes of the complex including T. jagerskioeldi sensu stricto, T. alcae Hoberg and Soudachanh, 2021, and T. sinistralis Hoberg and Soudachanh, 2021, along with 2 previously unrecognized taxa, are documented, occurring in 128 of 1976 seabirds examined (6%) and 17 of 41 marine avian species from 23 insular, coastal, and pelagic sites spanning the North Pacific. In completing an evaluation of this assemblage, we focus on those cestodes among 8 species of medium- to small-bodied alcids, subfamily Fraterculinae. Specimens designated as Tetrabothrius fraterculus n. sp. were observed among puffins (2 species of Fraterculus and Cerorhinca), whereas Tetrabothrius aithuia n. sp. is proposed for tapeworms in auklets (4 species of Aethia and Ptychoramphus) and a puffin (Cerorhinca); both cestodes are currently unknown among the Alcinae species of Cepphus, Uria, Brachyramphus, and Synthliboramphus based on the North Pacific inventory collections. These large-bodied cestodes, typical of the 5 species in the complex, are characterized among 46 currently valid species of Tetrabothrius in avian hosts, based on unique configurations of the genital atrium; male and female genital papillae; terminal genital ducts; numbers of testes; and the structure, position, and dimensions of the vaginal and atrial seminal receptacles. Ancillary characters contributing to differentiation include attributes of the scolex, structure, dimensions, and position of the vitelline gland and relative position of the dorsal and ventral osmoregulatory canals. A suite of complex attributes unequivocally separates 5 respective species that had historically been relegated to a single geographically widespread and morphologically variable taxon under T. jagerskioeldi sensu lato. Host range for respective cryptic species of the T. jagerskioeldi–complex reveal an intricate view of ecological isolation and connectivity across the greater North Pacific basin. Seabirds, marine mammals, and parasites are indicators of changing conditions over space and time. Oceanic regime shifts, prey cascades, and diversity for birds and parasites serve as proxies for revealing accelerating perturbation in marine foodwebs under climate forcing.
... The present approach consists, in a way, of examining the ancestral character-state reconstructions integrally, rather than separately. The idea of representing an entire anatomy as a combination of states in many characters is not by any means new; Hennig (1966) already coined the term "holomorph" for a similar concept. The ancestral anatomies-in the absence of methods to easily take into account dependences between charactersare typically reconstructed by separate optimization of the characters in the matrix. ...
This paper discusses methods to take into account interactions between characters, in the context of parsimony analysis. These interactions can be in the form of some characters becoming inapplicable given certain states of other, primary characters; in the form of only certain states being allowed in some characters when a given state or set of states occurs for other characters; or in the form of transformation costs in some character being higher or lower when other characters have certain states or transformations between states. Character–state reconstructions and evaluation of trees under the assumption of independence may easily lead to ancestral assignments that violate elementary rules of biomechanics, well‐established theories relating form and function or ideas about character co‐variation. An obvious example is reconstructing an ancestral bird as wingless and flying at the same time; another is reconstructing a protein‐coding gene as having a stop codon in some ancestors. If the characters are optimized independently, such chimeric ancestral reconstructions can occur even when no terminal displays the impossible combination of states. A set of conventions (implemented via new TNT commands and options) allows the definition of complex rules of interaction. By recoding groups of characters with proper step–matrix costs (and excluding impossible combinations from the set of permissible states), it is possible to find the ancestral reconstructions that maximize homology (and thus the degree to which similarities can be explained by common ancestry), within the constraints imposed by the rules specified by the user. We expect that considerations of biomechanics, functional morphology and natural history will be a source of many theories on possible character dependences, and that the present implementation will encourage users to take the possibility of character dependences into account in their phylogenetic analyses.
... As Michener and Sokal (1957, p. 131) pointed out, "If only a few characters are used, studies of relationships require weighting of certain conservative characters in the mental processes of the systematist." Later, exact phenetic methods that operate with non-equally weighted characters were designed (for example, Hartigan 1975, reviewed in De Soete et al. 1985DeSarbo et al. 1984reviewed in De Soete et al. 1985De Soete et al. 1985, see also Sokal 1986, p. 434). Therefore, the phenetic classification does not necessarily have to treat all characters as equally influential on the results. ...
The fundamental Hennigian principle, grouping solely on synapomorphy, is seldom used in modern phylogenetics. In the submitted paper, we apply this principle in reanalyzing five datasets comprising 197 complete plastid genomes (plastomes). We focused on the latter because plastome-based DNA sequence data gained dramatic popularity in molecular systematics during the last decade. We show that pattern-cladistic analyses based on complete plastid genome sequences can successfully resolve affinities between plant taxa, simultaneously simplifying both the genomic and analytical frameworks of phylogenetic studies. We developed “Matrix to Newick” (M2N), a program to represent the standard molecular alignment of plastid genomes in the form of trees or relationships directly. Thus, massive plastome-based DNA sequence data can be successfully represented in a relational form rather than as a standard molecular alignment. Application of methods of median supertree construction (the Average Consensus method has been used as an example in this study) or Maximum Parsimony analysis to relational representations of plastome sequence data may help systematist to avoid the complicated assumption-based frameworks of Maximum Likelihood or Bayesian phylogenetics that are most used today in massive plastid sequence data analyses. We also found that significant amounts of pure genomic information that typically accommodate the majority of current plastid phylogenomic studies can be effectively dropped by systematists if they focus on the pattern-cladistics or relational analyses of plastome-based molecular data. The proposed pattern-cladistic approach is a powerful and straightforward heuristic alternative to modern plastome-based phylogenetics.
... However, the search for well-founded criteria to quantify evolutionary changes without species splitting or the achievement of new adaptive qualities, and to translate them into classification rules, proved to be problematic. At least since Willi Hennig (Hennig 1950(Hennig , 1966 presented a logically sound methodology for the analysis of relationships, by distinguishing homologous similarities once again into original (plesiomorph) and derived (apomorph) ones, relative to the considered kin group, as the key point, a purely genealogical classification prevailed. The possibility of representing more information in one system was counterbalanced by the relief of finally having clear rules for naming groups. ...
Taxonomy is a science whose roots go back to the dawn of human curiosity. Its evergrowing body of knowledge, laid down in the biological classification, provides the framework within which every biologist operates. Taxonomists have always used the oldest scientific tools for their research - their natural capabilities of observation, gestalt perception, categorization, and classification - as well as the most advanced technologies of the day. Today, taxonomy is firmly anchored in evolutionary theory, spearheading on topics such as the species problem and biodiversity and its development.
... (vi) Monophyly of Agaonidae including Sycophaginae, which is supported by a complex of morphological and life-history traits (Bou cek, 1988;Heraty et al., 2013), and their association with figs. In essence, these benchmarks were used in a process of reciprocal illumination to assess the results of our current molecular and morphological hypotheses (Hennig, 1966;Mooi and Gill, 2016). ...
Chalcidoidea are mostly parasitoid wasps that include as many as 500 000 estimated species. Capturing phylogenetic signal from such a massive radiation can be daunting. Chalcidoidea is an excellent example of a hyperdiverse group that has remained recalcitrant to phylogenetic resolution. We combined 1007 exons obtained with Anchored Hybrid Enrichment with 1048 ultra-conserved elements (UCEs) for 433 taxa including all extant families, >95% of all subfamilies, and 356 genera chosen to represent the vast diversity of the superfamily. Going back and forth between the molecular results and our collective knowledge of morphology and biology, we detected bias in the analyses that was driven by the saturation of nucleotide data. Our final results are based on a concatenated analysis of the least saturated exons and UCE datasets (2054 loci, 284 106 sites). Our analyses support an expected sister relationship with Mymarommatoidea. Seven previously recognized families were not monophy-letic, so support for a new classification is discussed. Natural history in some cases would appear to be more informative than morphology, as illustrated by the elucidation of a clade of plant gall associates and a clade of taxa with planidial first-instar lar-vae. The phylogeny suggests a transition from smaller soft-bodied wasps to larger and more heavily sclerotized wasps, with egg parasitism as potentially ancestral for the entire superfamily. Deep divergences in Chalcidoidea coincide with an increase in insect families in the fossil record, and an early shift to phytophagy corresponds with the beginning of the "Angiosperm Terrestrial Revolution". Our dating analyses suggest a middle Jurassic origin of 174 Ma (167.3-180.5 Ma) and a crown age of 162.2 Ma (153.9-169.8 Ma) for Chalcidoidea. During the Cretaceous, Chalcidoidea may have undergone a rapid radiation in southern Gondwana with subsequent dispersals to the Northern Hemisphere. This scenario is discussed with regard to knowledge about the host taxa of chalcid wasps, their fossil record and Earth's palaeogeographic history.
Blastocrithidia triatomae is a monoxenic trypanosomatid parasite of triatomines, sharing the same insect vectors with Trypanosoma cruzi Chagas, 1909 and T. rangeli Tejera, 1920. It is known to cause a complex syndrome in insects which induces severe metabolic disorders and increasing in mortality rates. In the present study, we established an efficient serial axenic cultivation method for B. triatomae using a new medium, herein called MBT, which revealed previously unknown morphotypes, named microepimastigotes and sinemastigotes, not found in specific cell linage cultures. The results improve the knowledge on the life cycle of genus Blastocrithidia Laird 1959, its distinction from other trypanosomatids, such as T. cruzi and T. rangeli, and settle new ground for thorough exploration of morphological features and its application for trypanosomatid systematics.
This chapter discusses methods for incorporating DNA barcode information into formal taxonomic descriptions. We first review what a formal description entails and then discuss previous attempts to incorporate barcode information into taxonomic descriptions. Several computer programs are listed that extract diagnostics from DNA barcode data. Finally, we examine a test case (Astraptes taxonomy).
Filogenetik; biyoloji, genetik, kültürel arkeoloji, antropoloji ve dilbilim gibi alanlarda sıkça kullanılan, çeşitli organizma grupları arasındaki evrimsel ilişkiyi sınıflandırma yaparak sorgulayan etkili bir yöntemdir. Filogenetik, bireylerin veya grupların organizma evrimi ve çeşitliliğinin, ortak tarih ve ataları aracılığıyla birbirlerine nasıl ilişkilendirilebileceğini anlamak adına kullanılır. Evrimsel arka planı açısından, kültür fenomenin gelişimini inceleyen çalışmalar, Antik Dönem’e kadar geri götürülebilmektedir. Filogenetik yöntem kullanılarak, Darwin’in evrim kuramının etkisiyle kültür fenomeninin evrimleşmesini araştıran çalışmalar ise on dokuzuncu yüzyıl sonrasına aittir. Kültürel evrimleşme, doğası gereği kültürel etmenleri dikkate alarak anlaşılabilecek bir olgudur. Bu makalede ‘filogenetik’ yöntemin kuramsal altyapısı tartışılmış, bu yaklaşımın kültür alanına uygulanışını ‘dilbilim’ ile ilişkili olabilecek şekilde ele alan örnekler tartışılmıştır. Makale, Avustronezya ve Sahra altı Afrika’daki yerel dillerin evrimleşmesi ve maddi kültürleri arasındaki ilişkiyi filogenetik yöntem kullanarak tartışmaya açan örneklemleri ele alan ilk Türkçe çalışmadır. Makale, dilbilim alanında mevcut Türkçe literatüre nitelikli katkılar sunmaktadır. Makalede ele alınan, dil ailelerinin evrimleşme biçimleri hususundaki çıkarımlar Türkçe literatür için özgündür. Kültürel melezleşme, akrabalık tipolojileri-terminolojileri ve sayma sistemleri ile ilişkili olarak, Avustronezya ve Sahra altı Afrika’daki yerel dillerin evrimleşmesine dair çıkarımlar dilbilim ötesinde birçok disiplin için faydalı olabilecektir.
Frogs of the Allophrynidae are an enigmatic family from South America. To date, published information is lacking regarding this group’s reproductive biology and larval morphology. Here, we provide the first detailed description of the reproductive mode, developmental mode, and tadpole morphology for Allophryne ruthveni. We developed a captive breeding and rearing protocol for this species and then conducted a series of observations to describe aspects of its reproductive biology. In captivity, this species exhibits aquatic oviposition, where single eggs are laid ungrouped within a simple jelly capsule and are scattered free in the water column before sinking to develop on benthic substrates. We did not observe parental care nor any parental interactions with eggs post-fertilization. Tadpoles are characterized by an oval body, anteroventral oral disc, a labial tooth row formula of 2(2)/3, and a dextral vent tube. The buccopharyngeal cavity is marked by the presence of two pairs of infralabial papilla and four lingual papillae. Cranial morphology is characterized by the presence of the commissura quadratoorbital. This species possesses an additional slip of the m. rectus cervicis and of the m. levator arcuum branchialium III. We discuss our results in comparison with glassfrogs (Centrolenidae).
Three species of pocket mice (Chaetodipus artus, C. goldmani, and C. pernix) characterize the Sinaloan subregion of the Sonoran regional desert. They occur primarily in Sinaloan thornscrub and monsoon (dry deciduous) forest biotic communities, both of which have suffered from agricultural conversion. Sinaloan thornscrub occurs along the coastal plains of southern Sonora and Sinaloa, México, and grades into monsoon forest in the foothills of the Sierra Madre Occidental. We describe the geographical and ecological distributions of the 3 species of Chaetodipus, evaluate evolutionary relationships within each species based on mitochondrial DNA sequence data, and compare these to previously described phenetic, allozymic, and chromosomal variation. We elevate the subspecies of C. pernix to full species, delineate evolutionary units within C. goldmani and C. artus that we formally recognize as subspecies, and evaluate the conservation status of all 3 species of Chaetodipus.
The order Psocodea, including barklice, booklice, and parasitic lice, is diverse and widely distributed since the Cretaceous. That is particularly the case for the speciose extinct family Empheriidae (Psocodea, Trogiomorpha, Atropetae), recently fused with the ‘Archaeatropidae’. Understanding the evolution of barklice is dependent in part on studying this family, as its representatives have been found from the Early Cretaceous to the Eocene, surviving the K/Pg extinction event. The phylogenetic relationships of Empheriidae in relation to other families, such as Lepidopsocidae or Psoquillidae, have been extensively debated. However, distinguishing diagnostic characters for the Empheriidae has proven challenging. In this study, we describe the new empheriid Santonipsocus mimeticus gen. et sp. nov. from Cretaceous Charentese amber (France). It is the third empheriid species found in this locality. The new genus is compared with the other genera in the family, and Proprionoglaris guyoti and Proprionoglaris axioperierga are revised based on the type material and new specimens. We explore the phylogeny of Empheriidae, both the relationships with other families and the inner relationships between the genera, through maximum parsimony analysis and Bayesian inference analysis. Our results suggest that Empheriidae may represent a paraphyletic evolutionary grade to the rest of Atropetae. The phylogenetic relationships between genera align with the biogeography of the family and support previous hypotheses. In addition, we discuss the possible biology of the members of the family, shedding light on the evolutionary history of Empheriidae.
Triplets, as minimal informative rooted trees, are fundamental units of information in phylogenetics. Their importance for phylogenetic reconstruction, cladistic biogeography, or supertree methods relies on the fact that any rooted tree can be decomposed into a set of triplets. In order to formalize the tree building from a consistent triplet set, several k-adic rules of inference, i.e., rules that allow us to deduce at least one new triplet from exactly k other ones, have been identified. However, it remains unclear whether it is possible to reduce all the possible k-adic rules to a finite set of basic properties. In order to solve this problem, we propose here to define triplets in terms of degree of equivalence relations. Given the axiomatic definition of the latter, we establish a list of the most basic properties for triplets. With such an approach, we finally prove that the closure of any coherent triplet set can be computed uniquely from these basic properties.
Premise
Astragalus (Fabaceae), with more than 3000 species, represents a globally successful radiation of morphologically highly similar species predominant across the northern hemisphere. It has attracted attention from systematists and biogeographers, who have asked what factors might be behind the extraordinary diversity of this important arid‐adapted clade and what sets it apart from close relatives with far less species richness.
Methods
Here, for the first time using extensive phylogenetic sampling, we asked whether (1) Astragalus is uniquely characterized by bursts of radiation or whether diversification instead is uniform and no different from closely related taxa. Then we tested whether the species diversity of Astragalus is attributable specifically to its predilection for (2) cold and arid habitats, (3) particular soils, or to (4) chromosome evolution. Finally, we tested (5) whether Astragalus originated in central Asia as proposed and (6) whether niche evolutionary shifts were subsequently associated with the colonization of other continents.
Results
Our results point to the importance of heterogeneity in the diversification of Astragalus , with upshifts associated with the earliest divergences but not strongly tied to any abiotic factor or biogeographic regionalization tested here. The only potential correlate with diversification we identified was chromosome number. Biogeographic shifts have a strong association with the abiotic environment and highlight the importance of central Asia as a biogeographic gateway.
Conclusions
Our investigation shows the importance of phylogenetic and evolutionary studies of logistically challenging “mega‐radiations.” Our findings reject any simple key innovation behind high diversity and underline the often nuanced, multifactorial processes leading to species‐rich clades.
El presente estudio aborda la taxonomía y filogenia del género Pristimantis, perteneciente a la familia Craugastoridae, enfocándose en el grupo Pristimantis leptolophus. Este grupo, inicialmente esta compuesto por ocho especies endémicas de las Cordilleras Central y Occidental de Colombia, sin embargo, estos grupos presentan una notable diversidad específica que ha complicado los análisis morfológicos a gran escala. Tradicionalmente, la ausencia de sinapomorfías morfológicas ha dificultado la delimitación de grupos fenéticos dentro del género.
Implementamos metodologías como la transparentación y doble tinción de huesos y cartílagos, así como un análisis filogenético con la secuenciación de cuatro genes de 19 terminales. Estas técnicas permitieron una evaluación detallada de la monofilia del grupo Pristimantis leptolophus y de sus relaciones filogenéticas.
Los resultados obtenidos indican la parafilia del grupo en la filogenia molecular, contrastando con la monofilia observada en los análisis morfológicos y de evidencia total. Este hallazgo condujo a una reestructuración del grupo, incorporando diez especies descritas y cinco no descritas, y se identificaron dos sinapomorfías morfológicas que respaldan la agrupación en el análisis de evidencia total. Adicionalmente, se identificó un clado hermano, compuesto por especies del parafilético grupo P. lacrimosus. Este clado fue nombrado como grupo Pristimantis boulengeri, caracterizado por seis sinapomorfías distintivas. Este estudio proporcionó también descripciones exhaustivas de la morfología externa, osteología y caracteres miológicos para el grupo P. leptolophus, y efectuó comparaciones morfológicas con los grupos de especies myersi y devillei. Por último, se realizó una diagnosis del grupo de especies de P. boulengeri, compuesto por siete especies.
We report the first discovery of barklice preserved in copula from amber dating back to the mid-Cretaceous, thus documenting the oldest preserved reproductive behaviour of Psocodea. The new finding provides new insight into the evolution of copulatory behaviour in Trogiomorpha. Moreover, we describe and illustrate the new fossil material of Burmempheria densuschaetae (= Latempheria kachinensis) in the extinct family Empheriidae and Longiantennum fashengi in the extinct family Archaeatropidae, two diverse and widely distributed groups during the Cretaceous. No significant sexual dimorphism is recorded, apart from variation in size where males are larger. The taxonomy of Cretaceous empheriids from Burmese amber is revised and discussed.
Phylogeny is a model of the relationships between organisms, genes, proteins, or other structures based on common ancestry. It is also used for epidemiological investigations and analysis of parallel evolution between host and parasite. Phylogenetic trees can be visualized as dendrograms or as radial trees. The most important information read from a phylogenetic tree is the location of the different monophyletic groups. The main types of model parameters needed to construct a tree from a given dataset are the tree shape and the substitution matrix. One of the four types of phylogenetic methods (maximum parsimony, neighbor joining, maximum likelihood and Mr. Bayes) can then be used to construct the tree. The strength of trees can be evaluated by bootstrap analysis. The major data formats used as input for phylogenetic programs are presented as well as the major program packages. Finally, the reader is guided to the construct own neighbor joining tree.
Birds are so stable that they can rest and even sleep standing up. We propose that stable static balance is achieved by tensegrity. The rigid bones can be held together by tension in the tendons, allowing the system to stabilize under the action of gravity. We used the proportions of the bird's osteomuscular system to create a mathematical model. First, the extensor muscles and tendons of the leg are replaced by a single cable that follows the leg and is guided by joint pulleys. Analysis of the model shows that it can achieve balance. However, it does not match the biomechanical characteristics of the bird's body and is not stable. We then replaced the single cable with four cables, roughly corresponding to the extensor groups, and added a ligament loop at the knee. The model is then able to reach a stable equilibrium and the biomechanical characteristics are satisfied. Some of the anatomical features used in our model correspond to innovations unique to the avian lineage. We propose that tensegrity, which allows light and stable mechanical systems, is fundamental to the evolution of the avian body plan. It can also be used as an alternative model for bipedal robots.
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