Atelinae phylogenetic relationships: The trichotomy revived?

This research examines phylogenetic relationships between members of the Atelinae subfamily (Alouatta, Ateles, Brachyteles, and Lagothrix), based on analysis of three genetic regions. Two loci, cytochrome c oxidase subunit II (COII) and the hypervariable I portion of the control region, are part of the mitochondrial genome. The other is a single-copy nuclear gene, Aldolase A Intron V. Analysis of these genetic regions provides support for tribe Alouattini containing the Alouatta species, while tribe Atelini contains the other three genera. However, these three genetic regions produce conflicting results for relationships among tribe Atelini members. Previous genetic studies supported grouping Brachyteles with Lagothrix, leaving Ateles in a separate subclade. The present data sets vary based on the genetic region analyzed and method of analysis suggesting all possible cladistic relationships. These results are more consistent with investigations of morphology and behavior among these primates. The primary cause of discrepancy between this study and previous genetic studies is postulated to reside in increased sampling in the present study of genetic variation among members of the Atelinae, specifically Ateles. The present study utilized samples of Ateles from all postulated species for this genetically variable primate, while previous studies used only one or two species of Ateles. This paper demonstrates that shifting relationships are produced when different species of Ateles are used to reconstruct phylogenies. This research concludes that a trichotomy should still be supported between members of tribe Atelini until further analyses, which include additional Atelinae haplotypes are conducted.     

A Phylogenetic Study of Tribe Euphorbieae (Euphorbiaceae)

A phylogenetic investigation of a monophyletic lineage of spurge plants, tribe Euphorbieae, was conducted to elucidate evolutionary relationships, to clarify biogeographic patterns, and to reexamine the previous classification of Euphorbieae. Cladistic analyses of the 52 morphological characters of 61 species resulted in 2922 equally most parsimonious trees of 193 steps with a consistency index of 0.34. The strict consensus tree indicates genus Anthostema of subtribe Anthosteminae as a likely sister group to all other members of tribe Euphorbieae. The morphological data support a monophyletic origin of subtribe Euphorbiinae, but the subtribes Anthosteminae and Neoquillauminiinae did not form monophyletic groups. Although the previous taxonomic treatments within tribe Euphorbieae have supported the generic status of Pedilanthus, Monadenium, Synadenium, Chamaesyce, and Elaeophorbia, the results of this analysis do not support generic placement of them based on cladistic principles. Recognition of these groups as genera results in Euphorbia becoming a paraphyletic group. One solution to this problem in Euphorbieae is to divide the largest genus Euphorbia into several monophyletic genera and to keep the generic ranks for previously recognized genera. The distribution of basal endemic genera in Euphorbieae showed African and east Gondwanan affinities and strongly indicated that the ancestor of Euphorbieae originated prior to the breakup of Gondwanaland from an old group in Euphorbiaceae. However, some recent African taxa of Euphorbia should be interpreted by transoceanic dispersal from the New World ancestors.     

Morphological variation and phylogenetic relationships in the genus Anginon (Apiaceae)

The variation in habit and morphology of the twelve species of Anginon, a poorly known southern African genus of woody Apiaceae, is discussed and illustrated. The genus Glia is shown to be the obvious outgroup, sharing with Anginon two convincing synapomorphies: 1, the reduction or partial reduction of the laminar part of the leaves, and 2, the heavily cutinized outer walls of the fruit epidermis. Several characters of the internal structure of the fruit, together with other morphological characters, have been analysed by the cladistic method. Our interpretation of character evolution within the genus and a first hypothesis of phylogenetic relationships, showing three distinct infrageneric groups, is presented.     

Phylogenetic position of the southern African members of the tribe Psoraleeae based on molecular and morphological data

The tribe Psoraleeae (Leguminosae subfamily Papilionoideae) comprises 185 species in nine genera that have a nearly worldwide distribution, occurring predominantly in Mediterranean regions. About 60% of the species belong to the genera, Otholobium C.H.Stirt. and Psoralea L., which have a centre of diversity in the Cape Floristic Region of South Africa. Since previous molecular studies have sampled only a few species of the tribe from this region, this study sought to determine the phylogenetic position of the southern African genera and to test whether they are monophyletic. Phylogenetic relationships were reconstructed using DNA sequence data (trnL-F, rpoB-trnC and ITS) and seven morphological characters, which diagnose the two southern African genera. The data were analysed using the parsimony method. There was strong support for the Psoraleeae as a clade, but most of the nodes within the large genera were poorly supported. The southern African species of Psoralea and Otholobium together formed a strongly supported clade. This clade was sister to the genus Hoita Rydb., but without support. However, the Psoralea species were nested within the southern African Otholobium. Additionally, some South American species that are currently recognised as Otholobium were resolved in a clade distinct from the southern African species, making Otholobium polyphyletic. Morphological characters that separate Otholobium and Psoralea are discussed. Finally, the southern African genera as currently circumscribed are not monophyletic. However, further investigations using more informative DNA loci are required to validate this observation. Furthermore, the taxonomic placement of the South American species needs to be reviewed.     

Phylogeny of Parabuthus (Scorpiones, Buthidae)

A cladistic analysis of the 20 southern African species of Parabuthus Pocock, 1 890 (Scorpiones, Buthidae) and five of the eight north-eastern African and Arabian species is presented, based on 53 characters, mostly of the adult morphology. The resultant topology is largely congruent with Lamoral's (1978) unpublished topology for 14 Namibian species. Monophyly of the genus Parabuthus is supported, but monophyly of the disjunct southern African vs. north-eastern African and Arabian species is unsupported. The implications of the cladogram for understanding ecological specialization in Parabuthus , Afrotropical arid biogeography and Parabuthus envenomation are discussed.     

Untangling the phylogeny of neotropical lianas (Bignonieae, Bignoniaceae)

The tribe Bignonieae (Bignoniaceae) is a large and morphologically diverse clade of neotropical lianas. Despite being a conspicuous component of the neotropical flora, the systematics of the tribe has remained uncertain due to confusing patterns of morphological variation within the group. Chloroplast (ndhF) and nuclear (PepC) DNA sequences were used here to reconstruct the phylogeny of Bignonieae. Individual analyses of ndhF and PepC were highly similar to one another, yet localized differences in the placement of six species suggests some conflict between data sets. Combined analyses result in trees that are consistent with those from the individual analyses and provide greater support for the suggested relationships. This phylogeny provides important new insights into the systematics of the tribe. It identifies 21 strongly supported species groups, eight of which broadly correspond to currently recognized genera. In addition, each of these 21 species groups is supported by morphological synapomorphies. The consistency between morphological and molecular data suggests that the current phylogeny provides a solid framework for a formal revision of the generic-level classification and for addressing other aspects of the biology of Bignonieae.     

Phylogenetic analysis of the family Ariidae (Ostariophysi: Siluriformes), with a hypothesis on the monophyly and relationships of the genera

Ariid monophyly and intrafamilial relationships are investigated based on cladistic analysis of 230 morphological characters. Terminal taxa examined include whenever possible type‐species, or the most morphologically similar species to the type‐species of the nominal genera, and the largest possible number of species, including cleared and stained specimens, available in zoological collections. Previous hypotheses about monophyly of the Ariidae are strongly corroborated by new synapomorphies discovered in the present study. The subfamily Galeichthyinae and the remaining ariids are strongly supported by new morphological characters. The monotypic subfamily Bagreinae is recognized as the sister group to all nongaleichthyin ariids, supported by a large series of exclusive synapomorphies. A new concept of Ariinae is presented: the subfamily is found to be unequivocally monophyletic and includes all ariid genera, except Galeichthys and Bagre. New data supporting the monophyly of the genera included in the Ariinae are introduced and previous hypotheses of monophyly, species composition, morphological definition, and relationships are reviewed and discussed.     

Thermoregulatory patterns of two sympatric rodents: Otomys unisulcatus and Parotomys brantsii

1. The adaptations to an arid environment in two closely related rodent species were investigated. 2. The rate of oxygen consumption (VO2), body temperature (Tb), evaporative water loss and minimal conductance in Otomys unisulcatus and Parotomys brantsii were determined under controlled conditions at ambient temperatures (Ta), ranging from 11-31 C. 3. Physiological features atypical of desert-adapted rodents include a basal metabolic rate higher than predicted by body mass, the low "lower critical temperature" and symptoms of heat stress at 31 degrees C. 4. The low Tb and wide thermoneutral zone recorded for both species are characteristic of desert rodent species. 5. These species' physiological abilities reflect their mesic phylogeny and we suggest that behaviour must play an important role in their survival in semi-arid areas.     

Cladistic analysis of early Homo crania from Swartkrans and Sterkfontein, South Africa

The phylogenetic relationships of early Pleistocene Homo crania from the South African sites of Swartkrans and Sterkfontein were investigated through cladistic analyses of 99 morphological characters. The Swartkrans Member 1 specimen SK 847 and the Stw 53 cranium from Sterkfontein Member 5A were treated as separate operational taxonomic units (OTUs), distinct from the three species of early Homo-H. erectus, H. habilis, and H. rudolfensis-that are recognized from the Plio-Pleistocene deposits of East Africa. The cladistic analyses differed in the treatment of the South African OTUs (separate Swartkrans and Sterkfontein OTUs vs. a single Swartkrans+Sterkfontein OTU). PAUP 4.0 was used to construct cladograms and address hypotheses about relationships. In the analysis that treated the South African specimens as a single OTU, the position of that OTU was stable as a separate branch on the Homo clade between H. rudolfensis and [H. habilis+(H. erectus+H. sapiens)]. When SK 847 and Stw 53 were treated as separate OTUs, the majority of most parsimonious trees indicated that they were positioned in similar positions as the combined South African Homo OTU; that is, as separate branches between H. rudolfensis and [H. habilis+(H. erectus+H. sapiens)], with the Swartkrans OTU generally occupying a more derived position. The position of the Sterkfontein OTU was more stable than that of the Swartkrans OTU, which was found in several other positions among the minimum length trees. Running the analyses with only those characters preserved by SK 847 and Stw 53 resulted in similar topologies for minimum length trees, although the positions of Stw 53, SK 847, and H. habilis exchanged places in some trees. In no case was an exclusive sister relationship between either South African OTU and a particular species of Homo supported statistically. Both South African OTUs differ from H. habilis in the fewest number of cladistic characters.     

Molecular phylogenetics and evolution of host plant use in the Neotropical rolled leaf 'hispine' beetle genus Cephaloleia (Chevrolat) (Chrysomelidae: Cassidinae)

Here, we report the results of a species level phylogenetic study of Cephaloleia beetles designed to clarify relationships and patterns of host plant taxon and tissue use among species. Our study is based on up to 2088bp of mtDNA sequence data. Maximum parsimony, maximum likelihood, and Bayesian methods of phylogenetic inference consistently recover a monophyletic Cephaloleia outside of a basal clade of primarily palm feeding species (the 'Arecaceae-feeding clade'), and C. irregularis. In all three analyses, the 'Arecaceae-feeding clade' includes Cephaloleia spp. with unusual morphological features, and a few species currently placed in other cassidine genera and tribes. All three analyses also recover a clade that includes all Zingiberales feeding Cephaloleia and most Cephaloleia species (the 'Zingiberales-feeding clade'). Two notable clades are found within the 'Zingiberales-feeding clade.' One is comprised of beetles that normally feed only on the young rolled leaves of plants in the families Heliconiaceae and Marantaceae (the 'Heliconiaceae & Marantaceae-feeding clade'). The other is comprised of relative host tissue generalist, primarily Zingiberales feeding species (the 'generalist-feeding clade'). A few species in the 'generalist-feeding clade' utilize Cyperaceae or Poaceae as hosts. Overall, relatively basal Cephaloleia (e.g., the 'Arecaceae clade') feed on relatively basal monocots (e.g., Cyclanthaceae and Arecaceae), and relatively derived Cephaloleia (e.g., the 'Zingiberales-feeding clade') feed on relatively derived monocots (mostly in the order Zingiberales). Zingiberales feeding and specialization on young rolled Zingiberales leaves have each apparently evolved just once in Cephaloleia.     

PHYLOGENY AND BIOGEOGRAPHY OF CONDEEUM GROUP (PROTURA: PROTENTOMIDAE)

Abstract  Using the Hennig 86 phylogenetic analysis program to analyse the taxa in genera related to Condeellum , the phylogenetic relationships among the species are schemed on the basis of potential synapomorphies of the adults, represented by 16 characters. The character evolution and the route of dispersal are also discussed. The cladistic biogeographic analysis is performed. The basal taxon Condeellum exhibits an Indo-Pacific distribution and the sister group Neocondeellum species exhibit a collective Oriental and Holarctic distribution. The distribution patterns and the vicariance events occurred in those areas are hypothesized.     

康蚖群的系统发生和生物地理学的研究(原尾目:始蚖科)(英文)

应用HENNIG86系统发生分析程序,选择出成虫的有代表性的16个共同衍征,分析了与康蚖属相关各属的各个种类,得出了该类群的相关系统树。同时对特征的演化以及其扩散途径等也进行了讨论。文中还应用Page 1993的COMPONENT程序进行了生物地理学的分析;得到种类—地区支序图。其中康蚖属表现为典型的印度—太平洋分布型,而其姐妹群新康蚖属则兼有东洋区和全北区的分布型。至于分布地区的相互关系和在这些地区的分衍替代事件的发生等问题也作了初步的假想。     

Phylogenetic relationships of Carpha and its relatives (Schoeneae, Cyperaceae) inferred from chloroplast trnL intron and trnL-trnF intergenic spacer sequences

Within the tribe Schoeneae (Cyperaceae), the relationships between Carpha and its relatives have not been certain, and the limits and definition of Carpha have been controversial. Further, the relationships of species within Carpha have been unclear. In this study, cladistic analyses based on chloroplast trnL intron and trnL-trnF intergenic spacer sequence data were undertaken to estimate phylogenetic relationships in and around Carpha. This study found that Trianoptiles is sister to Carpha; Ptilothrix is sister to Cyathochaeta rather than to Carpha as suggested by some former authors; and Gymnoschoenus is distant from Carpha and its close relatives. The merging of Schoenoides back into Oreobolus is supported. The findings also revealed the non-monophyletic status of Costularia and of Schoenus, and indicated the phylogenetic relationships of species within Carpha.     

Phylogenetic analysis of Trechitae (Coleoptera: Carabidae) based on larval morphology, with a description of first-instar Phrypeus and a key to genera

Abstract. Sixty-nine characters of larval structure of twenty-eight genera of the supertribe Trechitae (Coleoptera: Carabidae) were analysed phylogenetically. The monophyly of Trechitae is strongly supported with five unique synapomorphies. The monophyly of Zolini + Bembidiini + Pogonini is supported with two synapomorphies. We propose that the tribe Trechini is a sister group to them and its monophyly is supported with two unique synapomorphies. The inferred branching pattern of Trechini genera is (Perileptus + Thalassophilus) + (Amblystogenium + (Trechimorphus + (Trechus + Epaphius + Aepopsis + Trechisibus))); Perileptus is a member of Trechodina rather than Trechina. The monophyly of Zolini is not supported. The monophyly of Pogonini is supported with two unique synapomorphies; its sister group relationships remain obscure; the branching pattern of pogonine genera is (((Pogonus + Pogonistes) + Cardiaderus) + Thalassotrechus). No evidence for monophyly of the tribe Bembidiini (s. lato; including subtribes Bembidiina, Tachyina, Xystosomina, and Anillina) was found. The relationships of Phrypeus are obscure; no evidence could be found linking it with Bembidiina. Without Phrypeus, Bembidiina might be a monophylum with a single synapomorphy. Sinechostictus branches basal of (Bembidion + Asaphidion) and therefore should be treated as a separate genus. Tachyina and Xystosomina form a monophylum based on two unique synapomorphies; a close relationship with a monophyletic Anillina is suggested. Reduction of the number of claws from two to one in Trechitae has taken place twice: within Trechina (Trechus, Epaphius, Aepopsis and Trechisibus) and in (Zolini + Bembidiini + Pogonini). The previously unknown larvae of the isolated genus Phrypeus are described and illustrated. A key to all twenty-eight analysed Trechitae genera based on characters of larvae and a list of larval autapomorphies for each genus are provided.     

Speciation mirrors geomorphology and palaeoclimatic history in African laminate-toothed rats (Muridae: Otomyini) of the Otomys denti and Otomys lacustris species-complexes in the 'Montane Circle' of East Africa

We adopted an integrated systematic approach to delimit evolutionary species and describe phylogeographic, morphometric and ecological relationships in Otomys denti (from the Albertine Rift, Southern Rift in Malawi and the northern Eastern Arc Mountains) and Otomys lacustris (from the Southern Rift in Tanzania and Zambia, and the southern Eastern Arc Mountains). Molecular [cytochrome (cyt) b sequences, 1143 bp, N  = 18], craniometric (classical, N  = 100 and geometric, N  = 60) and ecological (Partial Least Squares regression of shape and ecogeographic variables) approaches show a profound, parallel disjunction between two groups: (1) Eastern Arc and Southern Rift (including the Malawi Rift) ( O. lacustris and Otomys denti sungae ) and (2) Albertine Rift ( Otomys denti denti and Otomys denti kempi ) taxa. Within both groups, cyt b sequences or craniometric analysis provided evidence for the differentiation of both southern and northern Eastern Arc from Southern Rift lineages (across the so-called Makambako Gap). Within the Albertine Rift ( denti – kempi ) lineage, populations from individual mountain ranges differed significantly in skull shape (but not size), but were similar genetically. Over-reliance in the past on very few morphological characters (e.g. number of molar laminae) and a polytypic species concept has obscured phylogenetic relationships and species discrimination in this group. We recognize at least three species in this group, and distinct lineages within two of these species. Each species or lineage was endemic to one of three regions: the Albertine Rift, the Malawi Rift or the Eastern Arc. Our result echo conclusions of recent studies of other mammalian and bird taxa and reflect the geomorphology and palaeoclimatic history of the region.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 913–941.     

Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based on the chloroplast MATK coding sequence and flanking TRNK intron spacer regions

The tribe Acacieae (Fabaceae: Mimosoideae) contains two genera, the monotypic African Faidherbia and the pantropical Acacia, which comprise about 1200 species with over 950 confined to Australia. As currently recognized, the genus Acacia is subdivided into three subgenera: subg. Acacia, subg. Aculeiferum, and the predominantly Australian subg. Phyllodineae. Morphological studies have suggested the tribe Acacieae and genus Acacia are artificial and have a close affinity to the tribe Ingeae. Based on available data there is no consensus on whether Acacia should be subdivided. Sequence analysis of the chloroplast trnK intron, including the matK coding region and flanking noncoding regions, indicate that neither the tribe Acacieae nor the genus Acacia are monophyletic. Two subgenera are monophyletic; section Filicinae of subgenus Aculeiferum does not group with taxa of the subgenus. Section Filicinae, eight Ingeae genera, and Faidherbia form a weakly supported paraphyletic grade with respect to subg. Phyllodineae. Acacia subg. Aculeiferum (s. s.) is sister to the grade. These data suggest that characters currently used to differentiate taxa at the tribal, generic, and subgeneric levels are polymorphic and homoplasious in cladistic analyses.     

Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa

Recent discoveries of new fossil hominid species have been accompanied by several phylogenetic hypotheses. All of these hypotheses are based on a consideration of hominid craniodental morphology. However, Collard and Wood (2000) suggested that cladograms derived from craniodental data are inconsistent with the prevailing hypothesis of ape phylogeny based on molecular data. The implication of their study is that craniodental characters are unreliable indicators of phylogeny in hominoids and fossil hominids but, notably, their analysis did not include extinct species. We report here on a cladistic analysis designed to test whether the inclusion of fossil taxa affects the ability of morphological characters to recover the molecular ape phylogeny. In the process of doing so, the study tests both Collard and Wood's (2000) hypothesis of character reliability, and the several recently proposed hypotheses of early hominid phylogeny. One hundred and ninety-eight craniodental characters were examined, including 109 traits that traditionally have been of interest in prior studies of hominoid and early hominid phylogeny, and 89 craniometric traits that represent size-corrected linear dimensions measured between standard cranial landmarks. The characters were partitioned into two data sets. One set contained all of the characters, and the other omitted the craniometric characters. Six parsimony analyses were performed; each data set was analyzed three times, once using an ingroup that consisted only of extant hominoids, a second time using an ingroup of extant hominoids and extinct early hominids, and a third time excluding Kenyanthropus platyops. Results suggest that the inclusion of fossil taxa can play a significant role in phylogenetic analysis. Analyses that examined only extant taxa produced most parsimonious cladograms that were inconsistent with the ape molecular tree. In contrast, analyses that included fossil hominids were consistent with that tree. This consistency refutes the basis for the hypothesis that craniodental characters are unreliable for reconstructing phylogenetic relationships. Regarding early hominids, the relationships of Sahelanthropus tchadensis and Ardipithecus ramidus were relatively unstable. However, there is tentative support for the hypotheses that S. tchadensis is the sister taxon of all other hominids. There is support for the hypothesis that A. anamensis is the sister taxon of all hominids except S. tchadensis and Ar. ramidus. There is no compelling support for the hypothesis that Kenyanthropus platyops shares especially close affinities with Homo rudolfensis. Rather, K. platyops is nested within the Homo + Paranthropus + Australopithecus africanus clade. If K. platyops is a valid species, these relationships suggest that Homo and Paranthropus are likely to have diverged from other hominids much earlier than previously supposed. There is no support for the hypothesis that A. garhi is either the sister taxon or direct ancestor of the genus Homo. Phylogenetic relationships indicate that Australopithecus is paraphyletic. Thus, A. anamensis and A. garhi should be allocated to new genera.