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Abstract: Morris Goodman was a revolutionary. Together with a mere handful of like-minded scientists, Morris established himself as a leader in the molecular phylogenetic revolution of the 1960s. The effects of this revolution are most evident in this journal, which he founded in 1992. Happily for lemur biologists, one of Morris Goodman’s primary interests was in reconstructing the phylogeny of the primates, including the tooth-combed Lorisifomes of Africa and Asia, and the Lemuriformes of Madagascar (collectively referred to as the suborder Strepsirrhini). This paper traces the development of molecular phylogenetic and evolutionary genetic trends and methods over the 50-year expanse of Morris Goodman’s career, particularly as they apply to our understanding of lemuriform phylogeny, biogeography, and biology. Notably, this perspective reveals that the lemuriform genome is sufficiently rich in phylogenetic signal such that the very earliest molecular phylogenetic studies – many of which were conducted by Goodman himself – have been validated by contemporary studies that have exploited advanced computational methods applied to phylogenomic scale data; studies that were beyond imagining in the earliest days of phylogeny reconstruction. Nonetheless, the frontier still beckons. New technologies for gathering and analyzing genomic data will allow investigators to build upon what can now be considered a nearly-known phylogeny of the Lemuriformes in order to ask innovative questions about the evolutionary mechanisms that generate and maintain the extraordinary breadth and depth of biological diversity within this remarkable clade of primates. [Copyright &y& Elsevier]

Abstract: Phylogenetic hypotheses for the large cosmopolitan genus Hypericum (St. John’s wort) have previously been based on morphology, and molecular studies have thus far included only a few species. In this study, we used 360 sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (nrDNA) for 206 species representing Hypericum (incl. Triadenum and Thornea) and three other genera of Hypericaceae to generate an explicit phylogenetic hypothesis for the genus using parsimony and model-based methods. The results indicate that the small genus Triadenum is nested in a clade within Hypericum containing most of the New World species. Sister to Hypericum is Thornea from Central America. Within Hypericum, three large clades and two smaller grades were found; these are based on their general morphology, especially characters used previously in taxonomy of the genus. Relative to the most recent classification, around 60% of the sections of Hypericum were monophyletic. We used a Bayesian approach to reconstruct ancestral states of selected morphological characters, which resulted in recognition of characters that support major clades within the genus and a revised interpretation of morphological evolution in Hypericum. The shrubby habit represents the plesiomorphic state from which herbs evolved several times. Arborescent species have radiated convergently in high-elevation habitats in tropical Africa and South America. [Copyright &y& Elsevier]

Abstract: The genus Lygodactylus is a group of small, diurnal geckos distributed mainly in Africa and Madagascar. A closely related, monotypic genus is Microscalabotes from Madagascar. We examined fragments of two moderate- to slow-evolving nuclear genes (RAG-1, RAG-2) and of two fast-evolving mitochondrial genes (16SrRNA, cytochrome b) to estimate phylogenetic relationships among 28 (of about 60) species (including Microscalabotes). Since cytochrome b provided little resolution for analysis of interspecific relationships in Lygodactylus, it was excluded from the concatenated Bayesian analysis. Our well-resolved Bayesian inference tree and its resulting clades confirm many previously suggested relationships among dwarf geckos based mainly on morphological characters, while several novel relationships lead us to regroup some species and to synonymize the genus Microscalabotes with the genus Lygodactylus. Our phylogenetic analysis well supports the monophyly of Lygodactylus (including Microscalabotes). However, it rejects monophyly of the Madagascan Lygodactylus. On the other hand, the data do not reject monophyly of the African forms. Though Africa is currently the main centre of diversity of Lygodactylus, our data suggest that the most parsimonious scenario would be a Madagascan origin, one dispersal to Africa, and one back to Madagascar. [Copyright &y& Elsevier]

Abstract: Crabs of the family Hymenosomatidae are common in coastal and shelf regions throughout much of the southern hemisphere. One of the genera in the family, Hymenosoma, is represented in Africa and the South Pacific (Australia and New Zealand). This distribution can be explained either by vicariance (presence of the genus on the Gondwanan supercontinent and divergence following its break-up) or more recent transoceanic dispersal from one region to the other. We tested these hypotheses by reconstructing phylogenetic relationships among the seven presently-accepted species in the genus, as well as examining their placement among other hymenosomatid crabs, using sequence data from two nuclear markers (Adenine Nucleotide Transporter [ANT] exon 2 and 18S rDNA) and three mitochondrial markers (COI, 12S and 16S rDNA). The five southern African representatives of the genus were recovered as a monophyletic lineage, and another southern African species, Neorhynchoplax bovis, was identified as their sister taxon. The two species of Hymenosoma from the South Pacific neither clustered with their African congeners, nor with each other, and should therefore both be placed into different genera. Molecular dating supports a post-Gondwanan origin of the Hymenosomatidae. While long-distance dispersal cannot be ruled out to explain the presence of the family Hymenosomatidae on the former Gondwanan land-masses and beyond, the evolutionary history of the African species of Hymenosoma indicates that a third means of speciation may be important in this group: gradual along-coast dispersal from tropical towards temperate regions, with range expansions into formerly inhospitable habitat during warm climatic phases, followed by adaptation and speciation during subsequent cooler phases. [Copyright &y& Elsevier]

Abstract: The taxonomy of the African dwarf crocodile (genus Osteolaemus) has been disputed since a novel morphotype was discovered in the early 20th Century. Because this poorly-known reptile is widely hunted throughout the forests of Central and West Africa, resolving the existence and extent of taxonomic units has important management and conservation implications. Lack of molecular data from individuals of known origin and historical disagreement on diagnostic morphological characters have hindered attempts to settle one of the most important taxonomic questions in the Crocodylia. In an effort to clarify the evolutionary relationships among dwarf crocodiles, we sequenced three mitochondrial and two nuclear genes using a large sample of dwarf crocodiles from known localities across major drainage basins of forested Africa. Concordant results from Bayesian, maximum likelihood, maximum parsimony and population aggregation analytical methods support a previously recognized division of the dwarf crocodile into a Congo Basin form (O. osborni) and a West African form (Osteolaemus tetraspis), but also reveal a third diagnosable lineage from West Africa warranting recognition as an separate taxonomic unit. Corrected genetic distances between geographic regions ranged from 0.2% to 0.6% in nuclear fragments and 10.0 to 16.2% in mitochondrial COI. Population aggregation, using fixed and alternate character (nucleotide) states to cluster or divide populations, recovered 232 such molecular characters in 4286bp of sequence data and unambiguously aggregated populations into their respective geographic clade. Several previously recognized morphological differences coincide with our molecular analysis to distinguish Congo Basin crocodiles from the Ogooué Basin and West Africa. Discrete morphological characters have not yet been documented between the latter two regions, suggesting further work is needed or molecular data may be required to recognize taxonomic divisions in cases where putative species are morphologically cryptic. This study highlights the importance of using widespread taxon sampling and a multiple evidence approach to diagnose species boundaries and reveal cryptic diversity. [Copyright &y& Elsevier]

Abstract: Despite its large size (about 700 species), the australy-centred sedge tribe Schoeneae has received little explicit phylogenetic study, especially using molecular data. As a result, generic relationships are poorly understood, and even the monophyly of the tribe is open to question. In this study, plastid DNA sequences (rbcL, trnL–trnF, and rps16) drawn from a broad array of Schoeneae are analysed using Bayesian and parsimony-based approaches to infer a framework phylogeny for the tribe. Both analytical methods broadly support the monophyly of Schoeneae, Bayesian methods doing so with good support. Within the schoenoid clade, there is strong support for a series of monophyletic generic groupings whose interrelationships are unclear. These lineages form a large polytomy at the base of Schoeneae that may be indicative of past radiation, probably following the fragmentation of Gondwana. Most of these lineages contain both African and non-African members, suggesting a history of intercontinental dispersal. The results of this study clearly identify the relationships of the African-endemic schoenoid genera and demonstrate that the African–Australasian genus Tetraria, like Costularia, is polyphyletic. This pattern is morphologically consistent and suggests that these genera require realignment. [Copyright &y& Elsevier]