Ignacio H. Escapa

Unstable taxa in cladistic analysis: identification and the assessment of relevant characters

A common problem in phylogenetic analysis is the presence of unstable taxa that are depicted in multiple positions in optimal topologies. These uncertainties are reflected in strict consensus trees with polytomies that hamper the interpretation of the phylogenetic results. We propose a protocol for detecting unstable branches (either terminal taxa or clades) and identifying particular characters related to their instability in cladistic analysis. This procedure is based on an iterative evaluation of the agreement of triplets among the optimal topologies (i.e. most‐parsimonious trees, MPTs) and examination of character optimizations on these trees. Different types of characters underlying the unstable behaviour of taxa are detected: those with conflicting scorings that support alternative positions of problematic taxa and those with missing data in the unstable taxa that could reduce their instability if they are scored. The entire process is automated through a TNT script that provides a list of characters related to the instability of each unstable taxon. The outcome of this procedure can be used as a guide for further research efforts focused on the revision or addition of (morphological or molecular) phylogenetic data for elucidating the affinities of unstable taxa.

Phylogenetic Analysis of Araucariaceae: Integrating Molecules, Morphology, and Fossils

Premise of research. Phylogenetic relationships of Araucariaceae (Coniferophyta, Araucariales) are revised on the basis of the first combined data matrix for the family. Methodology. Taxon sampling includes 39 ingroup species (31 extant, 8 fossils) and outgroup species of all the remaining conifer families. Five fossil Araucaria species, one species of the genus Araucarites, and two species of the extinct genera Wairarapaia and Emwadea were included in the analyses. Character sampling includes 23 genomic regions (19 plastid, 2 nuclear, and 2 mitochondrial) and 62 morphological characters (52 discrete and 10 continuous). The phylogenetic analyses were conducted with equally weighted parsimony. Additionally, several analyses under different taxon- and gene-sampling regimes were analyzed for identifying the causes of the long-lasting controversies in the interrelationships of the three extant genera of Araucariaceeae. Pivotal results. Monophyletic Araucariaceae is the sister group of Podocarpaceae, forming the order Araucariales. Monophyly of Araucaria and Agathis is also strongly supported by the data. The results of both molecular and combined analyses indicate that Wollemia and Agathis form a clade (=agathioid clade) sister to Araucaria. Within Araucaria, the analyses support the monophyly of the four currently recognized sections: Araucaria, Bunya, Intermedia, and Eutacta. Results support the monophyly of living and fossil Araucaria (including Araucarites), whereas the remaining extinct genera are placed as the stem of the agathioid clade. In terms of the sensitivity analyses performed, results suggest that inconsistencies among previous results would be related to ingroup sampling. Conclusions. By means of a combined phylogenetic analysis, we have been able to obtain a strongly supported and well-resolved phylogeny of Araucariaceae that includes both living species and fossil species for the group. This study shows the feasibility and usefulness of phylogenetic analyses that incorporate multiple sources of evidence (molecules/morphology, living/fossil species, discrete/continuous characters).

Evolution and Relationships of the Conifer Seed Cone Telemachus: Evidence from the Triassic of Antarctica

The seed cone Telemachus is known from several Triassic localities in Gondwana. New specimens from two localities in Antarctica provide additional information about the type species, Telemachus elongatus, based on details of morphology and anatomy revealed by using a modified transfer technique on the compressed plants. Seed cones of T. elongatus are up to 6.0 cm long and characterized by conspicuous, elongate bracts. A second Antarctic species, described here as Telemachus antarcticus, is segregated, based on a shorter bract and differences in cone size. Newly recognized features of the genus include the shape, size, and disposition of the ovules; vascularization of the ovuliferous complex; and scale and bract histology. As a result of this new information, it is now possible to compare Telemachus with the permineralized Middle Triassic conifer seed cone Parasciadopitys from the Central Transantarctic Mountains. The similarities between the two genera make it possible to relate organs in different preservational modes and to develop a more complete concept for this widely distributed Gondwana conifer. Placing the Telemachus plant within a phylogenetic context makes it possible to evaluate the relationship with other so‐called transitional conifers, an informal group that has been interpreted as intermediate between Paleozoic and modern conifers.

Triassic floras of Antarctica: Plant diversity and distribution in high paleolatitude communities

ABSTRACT Continental Triassic sequences in Antarctica are among the most continuous and best represented in Gondwana. Triassic fossil plants have been collected sporadically from Antarctica since the beginning of the twentieth century, but our knowledge of the vegetation during this time has dramatically increased during the last three decades. Here we review the fossil record of Triassic plants as representatives of natural groups from sites along the Transantarctic Mountains, using the fossils as evidence for successive vegetational changes through the Triassic, taking into account that these plant communities were living under particular high-latitude (70° or higher) paleoclimatological conditions, including a polar light regime. Even though our knowledge of the Triassic floras of Antarctica is still incomplete, this survey shows that these floras were remarkably diverse. Lycopsids, equisetaleans, ferns, seed ferns, ginkgoaleans, and conifers were major components of the landscape in Antarctica during this time. The diversity of gymnosperms is exceptional, with almost every major clade of seed plants present, despite the high paleolatitude; however, each clade is often represented by only one or a few genera. The occurrence of permineralized peat, along with compression-impression floras, has increased our knowledge of the morphology, reproductive biology, and evolution of many of the plants in these floras. In general, floral changes in Antarctica during the Triassic can be recognized elsewhere in Gondwana, especially in South America, although a strict correlation based on macrofossils is still not possible. Thus, this contribution represents the first attempt to bring together information on Triassic floras from continental Antarctica (excluding the Antarctic Peninsula) within a biostratigraphic framework and thereby to compare these floras with those from lower latitudes.

First South American Agathis (Araucariaceae), Eocene of Patagonia

PREMISE OF THE STUDY Agathis is an iconic genus of large, ecologically important, and economically valuable conifers that range over lowland to upper montane rainforests from New Zealand to Sumatra. Exploitation of its timber and copal has greatly reduced the genuss numbers. The early fossil record of Agathis comes entirely from Australia, often presumed to be its area of origin. Agathis has no previous record from South America. METHODS We describe abundant macrofossils of Agathis vegetative and reproductive organs, from early and middle Eocene rainforest paleofloras of Patagonia, Argentina. The leaves were formerly assigned to the New World cycad genus Zamia. KEY RESULTS Agathis zamunerae sp. nov. is the first South American occurrence and the most complete representation of Agathis in the fossil record. Its morphological features are fully consistent with the living genus. The most similar living species is A. lenticula, endemic to lower montane rainforests of northern Borneo. CONCLUSIONS Agathis zamunerae sp. nov. demonstrates the presence of modern-aspect Agathis by 52.2 mya and vastly increases the early range and possible areas of origin of the genus. The revision from Zamia breaks another link between the Eocene and living floras of South America. Agathis was a dominant, keystone element of the Patagonian Eocene floras, alongside numerous other plant taxa that still associate with it in Australasia and Southeast Asia. Agathis extinction in South America was an integral part of the transformation of Patagonian biomes over millions of years, but the living species are disappearing from their ranges at a far greater rate.

Whole-Plant Concept and Environment Reconstruction of a Telemachus Conifer (Voltziales) from the Triassic of Antarctica

We present a whole-plant concept for a genus of voltzialean conifers on the basis of compression/impression and permineralized material from the Triassic of Antarctica. The reconstruction of the individual organs is based on a combination of organic connections, structural correspondences, similarities in cuticles and epidermal morphologies, co-occurrence data, and ex situ palynology. The affiliated genera of organs include trunks, branches, and roots (Notophytum); strap-shaped leaves with parallel venation (Heidiphyllum compressions and permineralized Notophytum leaves); seed cones (Telemachus and Parasciadopitys); pollen cones (Switzianthus); and bisaccate pollen of Alisporites type. Structural similarities lead us to suggest that Parasciadopitys is the permineralized state of a Telemachus cone and should be treated as a junior synonym. Biotic interactions involving the reconstructed conifer genus include plant-insect interactions (oviposition by Odonata) and not less than five different types of plant-fungal interactions, including two distinct endomycorrhizal associations, two probable seed parasites, and epiphyllous fungi. A representative whole plant is reconstructed as a 10–15-m-tall, seasonally deciduous forest tree with a vertical, narrow-conical crown shape. We interpret these Telemachus trees as the dominant components of peat-forming conifer swamps, forest bogs, and immature bottomland vegetation in the Triassic high-latitude river basins of southern Gondwana. In architecture, growth habit, and many ecological characteristics, the Telemachus conifers appear to be comparable to extant larch (Larix). Owing to the large amount and often exquisite preservation of the material, this conceptual whole-plant genus represents one of the most completely reconstructed ancient conifer taxa to date.

Pararaucaria delfueyoi sp nov from the late jurassic canadon calcareo formation, chubut, argentina: Insights into the evolution of the cheirolepidiaceae

The discovery of 16 cylindrical conifer seed cones at the Estancia Vilán locality in the Late Jurassic Cañadón Calcáreo Formation of Chubut Province, Patagonia, Argentina, provides anatomically preserved specimens, allowing for the description of a second species of Pararaucaria (Cheirolepidiaceae). The new species, Pararaucaria delfueyoi, is similar in general features to the type species, Pararaucaria patagonica, but has a specifically diagnostic combination of characters that include cone size, seed number, features of histology, and seed size. Specimens are cylindrical with a narrow axis that bears helically arranged bract/scale complexes. The bract and scale diverge from the axis at ∼90° and separate from each other almost immediately. The ovuliferous scale extends toward the margin of the cone and then arches over to enclose two inverted nonwinged seeds within a pocket of tissue. Although the specimens are abraded such that the distal regions of the ovuliferous scales are not preserved, this combination of morphological and histological characters allows for the assignment of P. delfueyoi to the Cheirolepidiaceae with confidence. The co-occurrence of this cone with an undescribed species of Araucaria extends the geographic and stratigraphic ranges of this association, which previously has been known only from the Middle Jurassic of Santa Cruz Province of Patagonia. This extends the knowledge of anatomical variation among seed cones of Cheirolepidiaceae and improves our understanding of homology relationships for conifer seed cone structures.

Fertile Osmundaceae from the Early Jurassic of Patagonia, Argentina

Two new compression-impression species of the Osmundaceae described from reproductive and vegetative remains are erected for the first time from the Early Jurassic of Argentina. Todites cacereii sp. nov. and Osmundopsis rafaelii sp. nov. demonstrate that two main osmundaceous reproductive morphologies; i.e., differentiated reduced or unreduced fertile laminae were already present and widespread in Gondwana by this time. On the basis of a discussion of relevant morphological characters, the phylogenetic meaning of the fossils Todites and Osmundopsis is explored. Likewise, the systematics and taxonomy of fossil taxa and their relationships with modern ones are discussed in light of current hypotheses. In this regard, because clear synapomorphies or apomorphies are not yet fully understood, it is suggested that fossil representatives are better placed in morphotaxa (Todites, Osmundopsis) than in any current genus. Nonetheless, the clear record of characters of the leptopteroid clade by the early Jurassic proves to be older than previously assumed, which also points to an earlier time of origination for the osmundaceous ferns.

A reappraisal of Neocalamites and Schizoneura (fossil Equisetales) based on material from the Triassic of East Antarctica

Sphenophytes are a common floral element in the Triassic of Gondwana. Most sphenophyte compression fossils have been conventionally assigned to a few, presumably very widespread species of Neocalamites based on vegetative features of the stems (or pith casts) and the foliage. During recent decades, however, new reports on morphological and anatomical details of some of these fossils have cast doubt on the systematic affinities of many Gondwanan Triassic sphenophytes. Here we describe Neocalamites suberosus (Artabe & Zamuner) nov. comb. et emend. and Schizoneura africana Feistmantel emend. from several Triassic deposits in the central Transantarctic Mountains and Victoria Land, East Antarctica. The material enables a critical reevaluation of morphological and anatomical features that have been historically used to define the two genera, including leaf-base morphology, degree of leaf fusion, stem vasculature and vallecular canals, and features of the nodal diaphragm. The diagnoses of Neocalamites and Schizoneura are emended so that they more accurately reflect recent advances in our understanding of the anatomy and ontogeny of these plants. [Benjamin Bomfleur [bbomfleur@ku]edu], Rudolph Serbet [serbet@ku.edu], Edith L. Taylor [etaylor@ku.edu] and Thomas N. Taylor [tntaylor@ku.edu], Department of Ecology and Evolutionary Biology, and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA; Ignacio H. Escapa [iescapa@mef.org.ar], CONICET—Museo Paleontológico Egidio Feruglio, Trelew, Chubut 9100, Argentina. Received 4.7.2012; revised 22.12.2012; accepted 7.1.2013. Bomfleur, B., Escapa, I.H., Serbet, R., Taylor, E.L. & Taylor, T.N., 2013. A reappraisal of Neocalamites and Schizoneura (fossil Equisetales) based on material from the Triassic of East Antarctica. Alcheringa 37, 1–17. ISSN 0311-5518.

Dealing with incompleteness: New advances for the use of fossils in phylogenetic analysis

The importance of fossils in understanding the evolutionary history of organisms was a controversial topic of debate during the first few decades in the history of phylogenetic systematics. During this time some authors suggested that extinct taxa could have only a minor role in phylogeny reconstruction (e.g., Patterson, 1981). For the most part, these types of bold statements were based on the fact that fossils are usually incomplete and, therefore, presumably not capable of overturning hypotheses based on the wealth of phylogenetic information that extant taxa provide. However, phylogenetic studies based only on extant organisms are certainly missing a large part of the diversity that arose during the evolutionary history of a taxonomic group and therefore use a highly biased sampling of the available information. The short history of phylogenetics, however, has shown that many heated discussions are put to rest with empirical data rather than by rhetorical debates. After several empirical studies clearly showed the critical role of fossils for understanding the evolution of major groups of organisms (Gauthier et al., 1988; Donoghue et al., 1989), advocates of ignoring fossil taxa in phylogenetic reconstruction rapidly disappeared (at least from the literature). The major reason for the importance of fossils in phylogenetic reconstruction is that they can bear unique combinations of characters, which are absent in extant taxa, and these can be critical to test the interrelationships of all analyzed species. This, in fact, is not a property exclusive of extinct organisms and the inclusion of extant taxa can be equally critical and necessary, depending on the characteristics of the phylogenetic problem being analyzed. In general terms, the importance of extinct taxa in phylogenetic reconstruction stems from the importance of achieving a taxon sampling scheme as complete as possible for solving a phylogenetic problem. In recent years increasing the …