Biogeographic patterns and phylogeography of dwarf chameleons (Bradypodion) in an African biodiversity hotspot

The southern African landscape appears to have experienced frequent shifts in vegetation associated with climatic change through the mid-Miocene and Plio-Pleistocene. One group whose historical biogeography may have been affected by these fluctuations are the dwarf chameleons (Bradypodion), due to their associations with distinct vegetation types. Thus, this group provides an opportunity to investigate historical biogeography in light of climatic fluctuations. A total of 138 dwarf chameleons from the Cape Floristic Region of South Africa were sequenced for two mitochondrial genes (ND2 and 16S), and resulting phylogenetic analyses showed two well-supported clades that are distributed allopatrically. Within clades, diversity among some lineages was low, and haplotype networks showed patterns of reticulate evolution and incomplete lineage sorting, suggesting relatively recent origins for some of these lineages. A dispersal-vicariance analysis and a relaxed Bayesian clock suggest that vicariance between the two main clades occurred in the mid-Miocene, and that both dispersal and vicariance have played a role in shaping present-day distributions. These analyses also suggest that the most recent series of lineage diversification events probably occurred within the last 3-6 million years. This suggests that the origins of many present-day lineages were founded in the Plio-Pleistocene, a time period that corresponds to the reduction of forests in the region and the establishment of the fynbos biome.     

Coming to America: multiple origins of New World geckos

Geckos in the Western Hemisphere provide an excellent model to study faunal assembly at a continental scale. We generated a time-calibrated phylogeny, including exemplars of all New World gecko genera, to produce a biogeographical scenario for the New World geckos. Patterns of New World gecko origins are consistent with almost every biogeographical scenario utilized by a terrestrial vertebrate with different New World lineages showing evidence of vicariance, dispersal via temporary land bridge, overseas dispersal or anthropogenic introductions. We also recovered a strong relationship between clade age and species diversity, with older New World lineages having more species than more recently arrived lineages. Our data provide the first phylogenetic hypothesis for all New World geckos and highlight the intricate origins and ongoing organization of continental faunas. The phylogenetic and biogeographical hypotheses presented here provide an historical framework to further pursue research on the diversification and assembly of the New World herpetofauna.     

Origin and in situ diversification in Hemidactylus geckos of the Socotra Archipelago

The Socotra Archipelago is an ancient continental fragment of Gondwanan origin and one of the most isolated landforms on Earth and a biodiversity hot spot. Yet, the biogeography and evolutionary history of its endemic fauna still remain largely overlooked. We investigate the origin, tempo and mode of diversification in the Hemidactylus geckos of the Socotra Archipelago. Concatenated and multilocus species coalescent analyses of Hemidactylus from Arabia and North Africa indicate that the Hemidactylus from Socotra do not form a monophyletic group and branch as three independent and well-supported clades instead. Both the chronogram inferred using the gene tree approach of BEAST and the age-calibrated multilocus species tree obtained using *BEAST suggest that the origin of Hemidactylus from Socotra may have involved a first vicariance event that occurred in the Early Miocene, followed by two independent transoceanic dispersal events that occurred more recently, during the Pliocene. Within Socotra, we analysed patterns of genetic diversity, the phylogeography and the demographic history in all seven nonintroduced species of Hemidactylus. Results based on two mitochondrial and two nuclear loci from 144 individuals revealed complex patterns of within-island diversification and high levels of intra-species genetic divergence. The interplay of both historical and ecological factors seems to have a role in the speciation process of this group of geckos. Interestingly, the case of H. forbesii and H. oxyrhinus, which inhabit the island of Abd al Kuri with an area of 133 km(2), may represent one of the most extreme cases of intra-island speciation in reptiles ever reported.     

Out-of-Africa origin and dispersal-mediated diversification of the butterfly genus Junonia (Nymphalidae: Nymphalinae)

The relative importance of dispersal and vicariance in the diversification of taxa has been much debated. Within butterflies, a few studies published so far have demonstrated vicariant patterns at the global level. We studied the historical biogeography of the genus Junonia (Nymphalidae: Nymphalinae) at the intercontinental level based on a molecular phylogeny. The genus is distributed over all major biogeographical regions of the world except the Palaearctic. We found dispersal to be the dominant process in the diversification of the genus. The genus originated and started diversifying in Africa about 20 Ma and soon after dispersed into Asia possibly through the Arabian Peninsula. From Asia, there were dispersals into Africa and Australasia, all around 5 Ma. The origin of the New World species is ambiguous; the ancestral may have dispersed from Asia via the Beringian Strait or from Africa over the Atlantic, about 3 Ma. We found no evidence for vicariance at the intercontinental scale. We argue that dispersal is as important as vicariance, if not more, in the global diversification of butterflies.     

The phylogeny of the 'higher' temnospondyls (Vertebrata: Choanata) and its implications for the monophyly and origins of the Stereospondyli

A parsimony analysis of 'higher' temnospondyls (all temnospondyls descended from the common ancestor of Eryops and Parotosuchus ) was performed using 37 terminal taxa and 121 osteological characters. Bremer support values for each internal node were calculated as a measure of clade strength. Additionally, the shortest trees that conformed to some alternative hypotheses were searched for. The following new taxa are established on the basis of the results: Euskelia (the clade containing the Eryopoidea and Dissorophoidea), Limnarchia (the clade containing Trimerorhachidae, Dvinosauroidea, Archegosauroidea and Stereospondyli), Dvinosauria (the clade containing Trimerorhachidae and Dvinosauroidea), Stereo-spondylomorpha (the clade containing Archegosauroidea and Stereospondyli), Capitosauria (the clade containing Lydekkerina and 'capitosauroids'), and Trematosauria (the clade containing Trematosauroidea, Rhytidosteidae, Plagiosauroidea, Metoposauroidea and Brachyopoidea). The monophyly of the assemblage of Mesozoic families called the Stereospondyli by Romer is supported. The dominance of the Stereospondyli in the Mesozoic and its rarity in the Palaeozoic is discussed. It is suggested that the radiation of the diverse stereospondyl clades, the Capitosauria and Trematosauria, began in the Late Permian of Gondwana, in a 'safe haven' that was less severely affected by the Late Permian extinction event. It is further speculated that the 'safe haven' was located in Antarctica, or possibly Australia.     

Biogeography of Southeast Asia and the West Pacific

The biogeography of Southeast Asia and the West Pacific is complicated by the fact that these are regions on the border of two palaeocontinents that have been separated for a considerable period of time. Thus, apart from any patterns of vicariance, two general patterns relating to dispersal can be expected: a pattern of Southeast Asian elements, perhaps of Laurasian origin, expanding into Australian areas, and a reverse pattern for Australian elements, perhaps of Gondwanan origin. On top of this, both Australian and Southeast Asian elements occur in the Pacific. They dispersed there as the Pacific plate moved westward, bringing the different islands within reach of Southeast Asia and Australia. In order to reconstruct the biotic history of these areas, two large data sets consisting of both plants and animals were generated, one for each pattern, which were analysed using cladistic methods. The general patterns that emerged were weakly supported and do not allow general conclusions.     

Evolutionary origins and diversification of proteobacterial mutualists

Mutualistic bacteria infect most eukaryotic species in nearly every biome. Nonetheless, two dilemmas remain unresolved about bacterial–eukaryote mutualisms: how do mutualist phenotypes originate in bacterial lineages and to what degree do mutualists traits drive or hinder bacterial diversification? Here, we reconstructed the phylogeny of the hyperdiverse phylum Proteobacteria to investigate the origins and evolutionary diversification of mutualistic bacterial phenotypes. Our ancestral state reconstructions (ASRs) inferred a range of 34–39 independent origins of mutualist phenotypes in Proteobacteria, revealing the surprising frequency with which host-beneficial traits have evolved in this phylum. We found proteobacterial mutualists to be more often derived from parasitic than from free-living ancestors, consistent with the untested paradigm that bacterial mutualists most often evolve from pathogens. Strikingly, we inferred that mutualists exhibit a negative net diversification rate (speciation minus extinction), which suggests that mutualism evolves primarily via transitions from other states rather than diversification within mutualist taxa. Moreover, our ASRs infer that proteobacterial mutualist lineages exhibit a paucity of reversals to parasitism or to free-living status. This evolutionary conservatism of mutualism is contrary to long-standing theory, which predicts that selection should often favour mutants in microbial mutualist populations that exploit or abandon more slowly evolving eukaryotic hosts.     

Comparative phylogeography of two coastal polychaete tubeworms in the Northeast Atlantic supports shared history and vicariant events

The historic processes which have led to the present-day patterns of genetic structure in the marine coastal fauna of the Northeast Atlantic are still poorly understood. While tectonic uplifts and changes in sea level may have caused large-scale vicariance, warmer conditions during glacial maxima may have allowed pockets of diversity to persist to a much wider extent than in the Northwestern Atlantic. The large-scale geographic distribution of deeply divergent lineages of the coastal polychaete tubeworms Pectinaria koreni (two clades) and Owenia fusiformis (three clades) were compared using a fragment of the mitochondrial cytochrome oxidase I gene (mtCOI). All lineages were present along the biogeographic transition zone on the north coast of Brittany (France) and we found evidence pointing towards congruence in the timing of cladogenic events between Pectinaria sp. (P. auricoma/P. belgica and P. koreni) and Owenia sp., suggesting a shared history of vicariant events. More conserved 16SrRNA sequences obtained from four species of Pectinariidae together with mtCOI sequences of P. koreni seem consistent with an initial establishment of pectinariids in the north, and a southward colonization of the Northeast Atlantic. Phylogeographic patterns in O. fusiformis were also consistent with a north/south pattern of lineage splitting and congruent levels of divergence were detected between lineages of both species. We observed signatures of both persistence in small northern glacial refugia, and of northwards range expansion from regions situated closer to the Mediterranean. However, whether the recolonization of the Northeast Atlantic by both species actually reflects separate interglacial periods is unclear with regards to the lack of molecular clock calibration in coastal polychaete species.     

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

Squamate reptiles (lizards and snakes) are one of the most diverse groups of terrestrial vertebrates. Recent molecular analyses have suggested a very different squamate phylogeny relative to morphological hypotheses, but many aspects remain uncertain from molecular data. Here, we analyse higher-level squamate phylogeny with a molecular dataset of unprecedented size, including 161 squamate species for up to 44 nuclear genes each (33 717 base pairs), using both concatenated and species-tree methods for the first time. Our results strongly resolve most squamate relationships and reveal some surprising results. In contrast to most other recent studies, we find that dibamids and gekkotans are together the sister group to all other squamates. Remarkably, we find that the distinctive scolecophidians (blind snakes) are paraphyletic with respect to other snakes, suggesting that snakes were primitively burrowers and subsequently re-invaded surface habitats. Finally, we find that some clades remain poorly supported, despite our extensive data. Our analyses show that weakly supported clades are associated with relatively short branches for which individual genes often show conflicting relationships. These latter results have important implications for all studies that attempt to resolve phylogenies with large-scale phylogenomic datasets.     

Vicariance, dispersal and scale in the aquatic subterranean fauna of karst regions

1. The causes of distribution patterns of stygobionts (obligate subterranean-dwelling aquatic species) were examined with special emphasis on vicariance and dispersal.
2. Dispersal was investigated on the premise that if migration is important, then migration at small scales should predict patterns at larger scales. Data on the copepod fauna of epikarst in Slovenia were especially useful for the study of migration, because data on habitat occupancy could be collected at scales of individual drips located metres apart to the scale of individual caves to entire karst regions. Occupancy of drips in one cave was a remarkably good predictor of occupancy of caves in a region, although not of the overall range of a given species. These results were also supported by occupancy patterns of the general stygobiotic fauna of West Virginia caves, compared at different scales.
3. Vicariance was investigated by noting that proximity to marine embayments increases the likelihood of vicariant speciation. In the U.S.A., only the fauna of the Edwards Aquifer of Texas has a significant component of marine-derived species. Differences in shape of the relationship between species number and number of caves in a county indicated that the marine-derived component represented an addition to rather than a replacement of the other stygobiotic species.
4. Thus, we found evidence for the importance of both vicariance and dispersal. The techniques employed could be used to study these patterns more generally, as more data become available.     

A multi-locus phylogeny reveals a complex pattern of diversification related to climate and habitat heterogeneity in southern African white-eyes

The recent, rapid radiation of Zosteropidae, coupled with their high levels of colonizing ability and phenotypic diversity, makes species delimitation within this family problematic. Given these problems, challenges to establish the mechanisms driving diversity and speciation within this group have arisen. Four morphologically distinct southern African Zosterops taxa, with a contentious taxonomic past, provide such a challenge. Here, supplemented with morphological and environmental analytical techniques, a combination of mitochondrial and nuclear markers were analyzed using Bayesian and Likelihood methods to determine their speciation patterns and to establish the phylogenetic relationships of these four morphologically diverse southern African Zosterops taxa. Nearly all individuals were phenotypically diagnosable, even those individuals collected in areas of contact between taxa. Localities where two or more taxa co-occur appear to possess intermediate environmental characteristics. Initial Bayesian and Likelihood mitochondrial DNA analyses and Bayesian structure analyses of the combined nuclear markers indicated levels of hybridization in areas of sympatry. A combined mtDNA and nuclear DNA analysis and a species tree analysis (with hybrids excluded) placed Z. pallidus as sister to the other southern African taxa, with Z. senegalensis the putative sister taxon to a clade comprising Z. capensis and Z. virens. The grouping of taxon-specific sampling localities and the apparent intermediate nature of birds from areas of sympatry points toward an influence of habitat type and the associated climatic conditions in driving Zosterops diversification in southern Africa.     

Evolution and biogeography of New Zealand's longjaw galaxiids (Osmeriformes: Galaxiidae): the genetic effects of glaciation and mountain building

1. The biological impact of glaciation in Southern Hemisphere freshwaters is poorly understood. Several large rivers of eastern South Island, New Zealand, represent a mosaic of glaciated and non-glaciated regions, and are thus well-suited for studies of post-glacial recolonization.
2. We conducted mtDNA analyses of South Island's endemic non-migratory longjaw galaxiids Galaxias prognathus and G. cobitinis (Osmeriformes: Galaxiidae) to test hypotheses of post-glacial recolonization, and to assess the vicariant effects of Pleistocene mountain building.
3. We analysed the phylogeography of longjaw cytochrome b sequences from 38 sites in central South Island ( n  = 83). On the basis of our sampling it seems that G. prognathus and G. cobitinis have a parapatric distribution in the Waitaki River system, their disjunction broadly coinciding with three large post-glacial lakes. Waitaki clades of both species are deeply divergent relative to conspecific taxa in drainages to the north and south.
4. Tests for recent population growth – predicted under post-glacial expansion of G. prognathus – do not refute recent recolonization of streams above glaciated lakes in the Waitaki River drainage. The apparent absence of potential 'source' populations from non-glaciated regions suggests a post-glacial population decline for G. prognathus below the Waitaki lakes.
5. Molecular clock calibrations based on several freshwater vicariant events elsewhere in New Zealand supported the geologically-derived hypothesis of Waitaki–Canterbury drainage isolation approximately 300 ka.     

Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting

Cichlid fishes are a key model system in the study of adaptive radiation, speciation and evolutionary developmental biology. More than 1600 cichlid species inhabit freshwater and marginal marine environments across several southern landmasses. This distributional pattern, combined with parallels between cichlid phylogeny and sequences of Mesozoic continental rifting, has led to the widely accepted hypothesis that cichlids are an ancient group whose major biogeographic patterns arose from Gondwanan vicariance. Although the Early Cretaceous (ca 135 Ma) divergence of living cichlids demanded by the vicariance model now represents a key calibration for teleost molecular clocks, this putative split pre-dates the oldest cichlid fossils by nearly 90 Myr. Here, we provide independent palaeontological and relaxed-molecular-clock estimates for the time of cichlid origin that collectively reject the antiquity of the group required by the Gondwanan vicariance scenario. The distribution of cichlid fossil horizons, the age of stratigraphically consistent outgroup lineages to cichlids and relaxed-clock analysis of a DNA sequence dataset consisting of 10 nuclear genes all deliver overlapping estimates for crown cichlid origin centred on the Palaeocene (ca 65–57 Ma), substantially post-dating the tectonic fragmentation of Gondwana. Our results provide a revised macroevolutionary time scale for cichlids, imply a role for dispersal in generating the observed geographical distribution of this important model clade and add to a growing debate that questions the dominance of the vicariance paradigm of historical biogeography.     

Molecular phylogeny, diversification and character evolution in Lupinus (Fabaceae) with special attention to Mediterranean and African lupines

Phylogenetic relationships within the complex genus Lupinus are estimated from internal transcribed spacer (ITS) sequences of the nuclear ribosomal DNA repeat. The molecular data supports Lupinus as a distinct monophyletic group within the tribe Genisteae. Different geographical lineages are revealed within Lupinus, which are each restricted to either the Old or the New World. In the New World, the ITS data support an eastern-western geographic disjunction of the lupines and the recognition of some well-supported clades. In the Old World, almost all the previously recognized taxa are taxonomically well differentiated. The homogeneous African rough-seeded lupines, Scabrispermae, are strongly supported as a monophyletic group, which is distinct from the diverse and heterogeneous circum-Mediterranean smooth-seeded ones. The latter appear to have evolved as two lineages, in which are revealed some intersectional relationships. Also ITS data allow the assessment of the phylogenetic position of the newly discovered species, L. anatolicus (in the Old World) and L. jaimehintoniana (the Mexican tree lupin). The ITS phylogeny suggests a rapid initial radiation of the lupines subsequent to their divergence from a common ancestor. Moreover, the results indicate that the annual and perennial habits have evolved many times in Lupinus and suggest a role for generation time in affecting the evolutionary history of lupines. Data on adaptive processes and character evolution are re-examined and discussed in the light of the ITS phylogeny.These studies were supported by the research unit UMR-CNRS 6553 Ecobio – University of Rennes (France), and by the NSERC of Canada (grant to R.J. Bayer, at the University of Alberta). They are greatfully acknowledged. All the persons that have contributed in different ways to this work on Lupinus, summarized in this presentation, are greatly thanked. Particularly, we would like to mention Malika Aïnouche, Roland Greinwald, André Huon, W.K. Swiecicki, Billie L. Turner and Ludger Witte for their contributions.     

Dispersal and diversity in the earliest North American sauropodomorph dinosaurs, with a description of a new taxon

Sauropodomorph dinosaurs originated in the Southern Hemisphere in the Middle or Late Triassic and are commonly portrayed as spreading rapidly to all corners of Pangaea as part of a uniform Late Triassic to Early Jurassic cosmopolitan dinosaur fauna. Under this model, dispersal allegedly inhibited dinosaurian diversification, while vicariance and local extinction enhanced it. However, apomorphy-based analyses of the known fossil record indicate that sauropodomorphs were absent in North America until the Early Jurassic, reframing the temporal context of their arrival. We describe a new taxon from the Kayenta Formation of Arizona that comprises the third diagnosable sauropodomorph from the Early Jurassic of North America. We analysed its relationships to test whether sauropodomorphs reached North America in a single sweepstakes event or in separate dispersals. Our finding of separate arrivals by all three taxa suggests dispersal as a chief factor in dinosaurian diversification during at least the early Mesozoic. It questions whether a 'cosmopolitan' dinosaur fauna ever existed, and corroborates that vicariance, extinction and dispersal did not operate uniformly in time or under uniform conditions during the Mesozoic. Their relative importance is best measured in narrow time slices and circumscribed geographical regions.     

Lygosomine phylogeny and the origins of Australian scincid lizards

Aim Australian scincid lizards represent three distinct groups within the cosmopolitan clade Lygosominae, the Egernia, Eugongylus and Sphenomorphus groups. This paper presents a time‐calibrated phylogeny for Lygosominae that provides the necessary temporal framework for assessing the contributions of immigration from Asia and of Gondwanan inheritance in the derivation of the Australian scincid fauna. Location Australasia, Asia, Africa. Methods Phylogenetic relationships and divergence times were inferred from novel BDNF, c‐mos and PTPN12 sequences (2408 aligned sites). Results Lygosomine monophyly is well supported, and there is strong support for monophyly of the Egernia, Eugongylus and Sphenomorphus groups. A sister‐group relationship of Tribolonotus (distributed in Melanesia and the Papuan Region) and the Egernia group is strongly supported in both Bayesian and maximum likelihood analyses. Australian representatives of the Sphenomorphus group compose a significantly supported clade estimated to have originated c. 25 Ma. An age of c. 18 Ma is inferred for a strongly supported clade comprising Australian representatives of the Egernia group; this clade diverged from Corucia zebrata (confined to the Solomon Islands) c. 25 Ma and from Tribolonotus c. 54 Ma. A well‐supported clade including all Australian Eugongylus group taxa sampled is estimated to have arisen c. 20 Ma. Main conclusions The Australian Sphenomorphus group is nested within the more inclusive Sphenomorphus group (distributed primarily in Asia and Australasia), suggesting comparatively recent descent from a colonizing Asian ancestor; the divergence times inferred here indicate that colonization occurred during the mid Cenozoic, subsequent to the rifting of Australia from Antarctica. An Oligocene origin of the extant Eugongylus group fauna of Australasia (the basal members of which are distributed in the Southwest Pacific) indicates that Eugongylus group lygosomines also dispersed to Australia relatively recently. The Egernia group diverged from Tribolonotus in the Early Eocene; however, extant Egernia group lygosomines originated only during the Late Oligocene, implying extensive pruning of stem taxa (i.e. extinction). As a result, inferences of the timing of dispersal into Australia are associated with substantial uncertainty, although independent palaeontological evidence suggests that the Egernia group entered Australia prior to the Oligocene, immediately after (or perhaps before) the separation of Australia and Antarctica.     

Higher plant origins and the phylogeny of green algae

Summary 5S rRNA sequences from six additional green algae lend strong molecular support for the major outlines of higher plant and green algae phylogeny that have been proposed under varying naming conventions by several authors. In particular, the molecular evidence now available unequivocally supports the existence of at least two well-separated divisions of the Chlorobionta: the Chlorophyta and the Streptophyta (i.e., charophytes) (according to the nomenclature of Bremer). The chlamydomonad 5S rRNAs are, however, sufficiently distinct from both clusters that it may ultimately prove preferable to establish a third taxon for them. In support of these conclusions 5S rRNA sequence data now exist for members of four diverse classes of chlorophytes. These sequences all exhibit considerably more phylogenetic affinity to one another than any of them show toward members of the other cluster, the Streptophyta, or the twoChlamydomonas strains. Among the Charophyceae, new 5S rRNA sequences are provided herein for three genera,Spirogyra, Klebsormidium, andColeochate. All of these sequences and the previously publishedNitella sequence show greater resemblance among themselves and to the higher plants than they do to any of the other green algae examined to date. These results demonstrate that an appropriately named taxon that includes these green algae and the higher plants is strongly justified. The 5S rRNA data lack the resolution needed, however, to unequivocally determine which of several subdivisions of the charophytes is the sister group of the land plants. The evolutionary diversity ofChlamydomonas relative to the other green algae was recognized in earlier 5S rRNA studies but was unanticipated by ultrastructural work. These new data provide further evidence for the relative uniqueness of the chlamydomonads and are discussed further.     

Distribution patterns and dispersal strategies of Galiciales

In Caliciales both passive and active spore dispersal occurs. A review of the distribution of 162 species is given. Species with small spores have wider distribution than species with large spores, irrespective of dispersal strategy. In antitropical species there is only rarely a differentiation between Northern and Southern Hemisphere populations. It is concluded that in several small-spored genera long-distance dispersal has been instrumental in dispersing the species and range extensions have been much more frequent than in large-spored species for which vicariance explanations are more appropriate. Comparisons with bryophyte distributions show differences in dispersal strategies and distribution patterns.