Geographical affinities of the Cape flora, South Africa

Aim The flora characteristic of the Cape Floristic Region (CFR) is dominated by a relatively small number of clades that have been proposed as ‘Cape clades’. These clades have variously been suggested to have African or Austral affinities. Here we evaluate the support for these conflicting hypotheses. In addition, we test the hypothesis that these clades share a common time of differentiation from their geographical neighbours. Location The Cape Floristic Region, South Africa Methods We use both published and unpublished phylogenetic information to investigate the geographical sister areas of the Cape clades as well as the timing and the direction of biogeographical disjunctions. Results Almost half of the Cape clades for which unambiguous sister areas could be established show a trans‐Indian Ocean disjunction. The earliest trans‐Indian Ocean disjunction dates from 80 Ma. Other disjunctions date from various times in the Cenozoic, and we suggest that the process of recruiting lineages into the Cape flora might be ongoing. Relatively few Cape clades show a sister relationship with South America and tropical Africa, despite their relative geographical proximity. Numerous Cape clades contain species also found on tropical African mountains; in all cases tested, these species are shown to be embedded within the Cape clades. While many Cape clades show a relationship with the Eurasian temperate flora, this is complicated by their presence in tropical Africa. The single case study addressing this to date suggests that the Cape clade is nested within a European grade. Main conclusions Although many Cape clades show Austral rather than African relationships, there are numerous other patterns suggestive of a cosmopolitan flora. This spatial variation is echoed in the temporal data, from which, although there is wide variance around the dates of disjunctions, it is clear the Cape flora has been assembled over a long time period. There is no simple hypothesis that can account for the geographical sources of the currently distinctive Cape flora. The phylogenetic positions of Afromontane members of Cape clades suggest a history of dispersal from the CFR, rather than the reverse.     

Dispersal, vicariance, and timing of diversification in Nothonotus darters

The species diversity of North American freshwater fishes is unparalleled among temperate regions of the planet. This diversity is concentrated in the Central Highlands of eastern North America and this distribution pattern has inspired different models involving either dispersal or vicariance to explain the high species diversity of North American fishes. The most popular of these models is the Central Highlands vicariance hypothesis (CHVH), which proposes an ancient and diverse widespread fauna that existed across a previously continuous highland landscape that is much different from today. The mechanisms of isolation in the CHVH involve specific instances of vicariance that affected several diverse lineages of Central Highlands fishes. We tested predictions of the CHVH and alternative models using a cytochrome b-inferred phylogeny of the darter clade Nothonotus. A Bayesian mixed-model method was used for phylogenetic analysis. The phylogenetic data set included all 20 recognized Nothonotus species, and most species were represented with multiple sequences. We were able to convert genetic branch lengths to absolute age using external fossil calibrations in the freshwater perciform fish clade Centrarchidae. Using a well-resolved Nothonotus phylogeny and divergence time estimates, we identify equal numbers of instances of both vicariance and dispersal among disjunct regions of the Central Highlands, biogeographic pseudocongruence, rather recent speciation in Nothonotus, and a surprisingly large amount of speciation within highland areas. With regard to Nothonotus, previous Central Highlands biogeographic models offer little in the way of providing possible mechanisms responsible for diversification in the clade. Patterns of speciation in Nothonotus are similar to those discovered in recent efforts that have included speciation as a parameter into classic models of island biogeography.     

First fossil Molinaranea Mello‐Leitão, 1940 (Araneae: Araneidae), from middle Miocene Dominican amber,with a phylogenetic and palaeobiogeographical analysis of the genus

The first fossil Molinaranea is described, from middle Miocene Dominican amber. This record extends the known range of the genus back 16 million years; it also extends the geographical range of the genus through time, with extant species known only from Chile, Argentina, the Falkland Islands, and Juan Fernandez Island. A parsimony‐based phylogenetic analysis was performed, which indicates that the fossil species, Molinaranea mitnickii sp. nov. , is nested with Molinaranea magellanica Walckenaer, 1847 and Molinaranea clymene Nicolet, 1849 . A modified Brooks parsimony analysis was conducted in order to examine the biogeography and origins of the fossil species in the Dominican Republic; the analysis suggests that M. mitnickii sp. nov. arrived in Hispaniola from South America as a result of a chance dispersal event. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 711–725.     

Vicariance and endemism in a Neotropical savanna hotspot: distribution patterns of Cerrado squamate reptiles

Aim To test predictions of the vicariance model, to define basic biogeographical units for Cerrado squamates, and to discuss previous biogeographical hypotheses. Location Cerrado; South American savannas south of the Amazon, extending across central Brazil, with marginal areas in Bolivia and Paraguay and isolated relictual enclaves in adjacent regions. Methods We compiled species occurrence records via field sampling and revision of museum specimens and taxonomic literature. All species were mapped according to georeferenced locality records, and classified as (1) endemic or non‐endemic, (2) typical of plateaus or depressions, and (3) typical of open or forested habitats. We tested predictions of the vicariance model using biotic element analysis, searching for non‐random clusters of species ranges. Spatial congruence of biotic elements was compared with putative areas of endemism revealed by sympatric restricted‐range species. Effects of topographical and vegetational mosaics on distribution patterns were studied according to species composition in biotic elements and areas of endemism. Results We recorded 267 Cerrado squamates, of which 103 (39%) are endemics, including 20 amphisbaenians (61% endemism), 32 lizards (42%) and 51 snakes (32%). Distribution patterns corroborated predictions of the vicariance model, revealing groups of species with significantly clustered ranges. An analysis of endemic species recovered seven biotic elements, corroborating results including non‐endemics. Sympatric restricted‐range taxa delimited 10 putative areas of endemism, largely coincident with core areas of biotic elements detected with endemic taxa. Distribution patterns were associated with major topographical and vegetational divisions of the Cerrado. Endemism prevailed in open, elevated plateaus, whereas faunal interchange, mostly associated with forest habitats, was more common in peripheral depressions. Main conclusions Our results indicate that vicariant speciation has strongly shaped Cerrado squamate diversity, in contrast to earlier studies emphasizing faunal interchange and low endemism in the Cerrado vertebrate fauna. Levels of squamate endemism are higher than in any other Cerrado vertebrate group. The high number of recovered endemics revealed previously undetected areas of evolutionary relevance, indicating that biogeographical patterns in the Cerrado were poorly represented in previous analyses. Although still largely undocumented, effects of vicariant speciation may be prevalent in a large fraction of Cerrado and Neotropical biodiversity.     

Historical biogeography and phylogeny of monachine seals (Pinnipedia: Phocidae) based on mitochondrial and nuclear DNA data

Aim To determine the origin and diversification of monachine seals using a phylogenetic framework. Methods Molecular sequence data from three mitochondrial genes (cyt b, ND1 and 12S), and one nuclear marker (an intron from the α‐lactalbumin gene) were examined from all extant species of monachine seals. Maximum likelihood and partitioned Bayesian inference were used to analyse separate and combined (mitochondrial + nuclear) data sets. Divergence times were estimated from the resultant phylogeny using nonparametric rate smoothing as implemented by the program r8s. Results Mirounga, Monachus and the Lobodontini form three well‐supported clades within a monophyletic Monachinae. Lobodontini + Mirounga form a clade sister to Monachus. Molecular divergence dates indicate that the first split within the Monachinae (Lobodontini + Mirounga clade and Monachus) occurred between 11.8 and 13.8 Ma and Mirounga, Monachus and the Lobodontini originated 2.7–3.4, 9.1–10.8 and 10.0–11.6 Ma, respectively. Main conclusions Two main clades exist within Monachinae, Monachus and Lobodontini + Mirounga. Monachus, a warm water clade, originated in the North Atlantic and maintained the temperate water affinities of their ancestors as they diversified in the subtropic regions of the Northern Hemisphere. The cold‐water clade, Lobodontini + Mirounga, dispersed southward to the cooler climates of the Southern Hemisphere. The Lobodontini continued south until reaching the Antarctic region where they diversified into the present‐day fauna. Mirounga shows an anti‐tropical distribution either reflective of a once cosmopolitan range that was separated by warming waters in the tropics or of transequatorial dispersal.     

Revisiting the phylogeny of Ranunculeae: Implications for divergence time estimation and historical biogeography

Previous studies based on different molecular datasets have generated conflicting topologies for Ranunculeae. Here, we revisit the phylogeny of Ranunculeae by analyzing the individual matK/trnK, psbJ-petA, and internal transcribed spacer (ITS) data, the combined matK/trnK, psbJ-petA, and ITS dataset, and the combinedrbcL, trnL-F, matK/trnK, psbJ-petA, and ITS dataset. Based on the tree-based comparisons, blast searches against NCBI of the sequences, and close examination of the alignment, we found that 10 psbJ-petA sequences previously used were questionable (erroneous or problematic) and responsible for previous conflicting topologies. After omitting these questionable sequences, we provide a new phylogeny for Ranunculeae, in which Beckwithia–Cyrtorhyncha, Kumlienia, andPeltocalathos were replaced. These new replacements are supported by corresponding morphological characters. Moreover, three previously proposed intercontinental disjunct distributions within Ranunculus were also refuted. In our framework, our divergence time and biogeographic analyses indicate that divergence time estimates and the ancestral areas reconstructed for 10 of the 15 nodes in the genus-level phylogeny were influenced by elimination of the questionable sequences. The most recent common ancestor of Ranunculeae was inferred to be present in Europe and North America during the late Eocene. Clades I and II began to diversify in Europe and North America, respectively, and subsequently migrated to other continents. This study shows that it is necessary to analyze individual chloroplast DNA region datasets separately to detect questionable sequences early in the study. The combined dataset including the questionable sequences resulted in an erroneous phylogenetic tree, and the use of this tree subsequently affected age estimates and biogeographic analyses.     

Inferences of biogeographical histories within subfamily Hyacinthoideae using S-DIVA and Bayesian binary MCMC analysis implemented in RASP (Reconstruct Ancestral State in Phylogenies)

Background and Aims

Subfamily Hyacinthoideae (Hyacinthaceae) comprises more than 400 species. Members are distributed in sub-Saharan Africa, Madagascar, India, eastern Asia, the Mediterranean region and Eurasia. Hyacinthoideae, like many other plant lineages, show disjunct distribution patterns. The aim of this study was to reconstruct the biogeographical history of Hyacinthoideae based on phylogenetic analyses, to find the possible ancestral range of Hyacinthoideae and to identify factors responsible for the current disjunct distribution pattern.

Methods

Parsimony and Bayesian approaches were applied to obtain phylogenetic trees, based on sequences of the trnL-F region. Biogeographical inferences were obtained by applying statistical dispersal-vicariance analysis (S-DIVA) and Bayesian binary MCMC (BBM) analysis implemented in RASP (Reconstruct Ancestral State in Phylogenies).

Key Results

S-DIVA and BBM analyses suggest that the Hyacinthoideae clade seem to have originated in sub-Saharan Africa. Dispersal and vicariance played vital roles in creating the disjunct distribution pattern. Results also suggest an early dispersal to the Mediterranean region, and thus the northward route (from sub-Saharan Africa to Mediterranean) of dispersal is plausible for members of subfamily Hyacinthoideae.

Conclusions

Biogeographical analyses reveal that subfamily Hyacinthoideae has originated in sub-Saharan Africa. S-DIVA indicates an early dispersal event to the Mediterranean region followed by a vicariance event, which resulted in Hyacintheae and Massonieae tribes. By contrast, BBM analysis favours dispersal to the Mediterranean region, eastern Asia and Europe. Biogeographical analysis suggests that sub-Saharan Africa and the Mediterranean region have played vital roles as centres of diversification and radiation within subfamily Hyacinthoideae. In this bimodal distribution pattern, sub-Saharan Africa is the primary centre of diversity and the Mediterranean region is the secondary centre of diversity. Sub-Saharan Africa was the source area for radiation toward Madagascar, the Mediterranean region and India. Radiations occurred from the Mediterranean region to eastern Asia, Europe, western Asia and India.     

Dispersal,fragmentation, and isolation shape the phylogeography of the European lineages of Polyommatus (Agrodiaetus) ripartii (Lepidoptera: Lycaenidae)

Polyommatus ripartii is a biogeographically and taxonomically poorly understood species of butterfly with a scattered distribution in Europe. Recently, it has been shown that this species includes several European endemic and localized taxa (galloi, exuberans, agenjoi) that were previously considered species and even protected, a result that poses further questions about the processes that led to its current distribution. We analysed mitochondrial DNA and the morphology of P. ripartii specimens to study the phylogeography of European populations. Three genetically differentiated but apparently synmorphic lineages occur in Europe that could be considered evolutionarily significant units for conservation. Their strongly fragmented and counterintuitive distribution seems to be the result of multiple range expansions and contractions along Pleistocene climatic oscillations. Remarkably, based on the 79 specimens studied, these genetic lineages do not seem to extensively coexist in the distributional mosaic, a phenomenon most evident in the Iberian Peninsula. One of the important gaps in the European distribution of P. ripartii is reduced by the discovery of new Croatian populations, which also facilitate a better understanding of the biogeography of the species. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 817‐829.     

Social but lonely: Species delimitation of social voles and the evolutionary history of the only Microtus species living in Africa

The social vole of Cyrenaica, Libya, is the only extant representative of the Cricetidae family found in Africa. Its taxonomic status has been under debate, partly due to the problematic systematics of the entire group of social voles and partly due to the lack of morphological and molecular data from Cyrenaican specimens. In this study, we applied ancient DNA protocols to produce three cytochrome b (cytb) sequences of Cyrenaican voles and built a phylogenetic reconstruction (195 sequences in total) incorporating all available cytb sequences of the remaining social voles, other representatives of the genus Microtus and closely related cricetids. We used this phylogeny to test the performance of the model-based, single-locus, species delimitation approach implemented in mPTP and delimited nine species of social voles. Among them are the Cyrenaican vole, Microtus mustersi and its sister species M. guentheri, distributed along the Mediterranean coasts of southwestern Asia. Biogeographical reconstruction of ancestral area and molecular clock estimations of the time since the divergence of the two sister lineages suggest that their common ancestor dispersed into Africa through a coastal route and was isolated in Cyrenaica as a result of population fragmentation associated with Middle Pleistocenic pluvial/interpluvial cycles. Geographic isolation triggered the speciation process, but species distribution modeling gave evidence of subsequent niche divergence; M. guentheri has adapted to the xeric conditions of its distributional area, while M. mustersi benefited from the milder Cyrenaican climate. The Cyrenaican vole is a relict species more than 200,000 years old, has a small and isolated distribution and probably merits conservation.     

Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus)

Four distinct phylogeographical patterns across Southeast Asia were observed for four species of seahorse (genus Hippocampus) with differing ecologies. For all species, genetic differentiation (based on cytochrome b sequence comparisons) was significantly associated with sample site (Phi(ST) = 0.190-0.810, P < 0.0001) and with geographical distance (Mantel's r = 0.37-0.59, P < 0.019). Geographic locations of genetic breaks were inconsistent across species in 7/10 comparisons, although some similarities across species were also observed. The two shallow-water species (Hippocampus barbouri and Hippocampus kuda) have colonized the Sunda Shelf to a lesser degree than the two deeper-water species (Hippocampus spinosissimus and Hippocampus trimaculatus). In all species the presence of geographically restricted haplotypes in the Philippines could indicate past population fragmentation and/or long-distance colonization. A nested clade analysis (NCA) revealed that long-distance colonization and/or fragmentation were likely the dominant forces that structure populations of the two shallow-water species, whereas range expansion and restricted dispersal with isolation by distance were proportionally more important in the history of the two deeper-water species. H. trimaculatus has the most widespread haplotypes [average clade distance (D(c)) of nonsingleton haplotypes = 1169 km], indicating potentially high dispersal capabilities, whereas H. barbouri has the least widespread haplotypes (average D(c) = 67 km) indicating potentially lower dispersal capabilities. Pleistocene separation of marine basins and postglacial flooding of the Sunda Shelf are extrinsic factors likely to have contributed to the phylogeographical structure observed, whereas differences among the species appear to reflect their individual ecologies.     

New light into the hormogastrid riddle: morphological and molecular description of Hormogaster joseantonioi sp. n. (Annelida,Clitellata, Hormogastridae)

The earthworm family Hormogastridae shows a remarkable disjunction in its distribution in the Iberian Peninsula, with the Hormogaster elisae species complex isolated from the rest of the species. Hormogaster joseantonioi sp. n., a new species found in the intermediate area between the main ranges (in Teruel, Aragón), was described following the integrative approach, as it is suitable for earthworms due to their highly homoplasic morphology. The phylogenetic analysis of the molecular markers placed the new species as a sister taxon to H. elisae, thus showing the colonizing lineage of Central Iberian Peninsula could have originated near the H. joseantonioi sp. n. current range. External morphological characters revealed some degree of overlap with previously described species, but internal characters presented configurations/states unknown from other members of the family. These traits make the new species a key piece to understand the evolution of Hormogastridae.     

Temporal,spatial and ecological dynamics of speciation among amphi‐Beringian small mammals

Aim

Quaternary climate cycles played an important role in promoting diversification across the Northern Hemisphere, although details of the mechanisms driving evolutionary change are still poorly resolved. In a comparative phylogeographical framework, we investigate temporal, spatial and ecological components of evolution within a suite of Holarctic small mammals. We test a hypothesis of simultaneous divergence among multiple taxon pairs, investigating time to coalescence and demographic change for each taxon in response to a combination of climate and geography.

Location

Beringia, the nexus of the northern continents.

Methods

We used approximate Bayesian computation methods to test for simultaneous divergence among eight pairs of taxa, using cytochrome b gene sequences. We calculated coalescence times for eastern and western components of each pair and for the combined pairs, and relate dates to Quaternary climatic periodicity and combinations of environmental events and physical barriers. Population growth and expansion statistics were used to test evolutionary responses among taxa, including range shifts, persistence or periodic extirpation. Species distribution models (SDMs) for each taxon were used to predict their geographical ranges during the present interglacial, Last Glacial Maximum and previous interglacial.

Results

Multiple divergence events across Beringia were primarily coincident with extreme glacial cycles of the late Quaternary. Structure within Beringia is spatially consistent with at least three environmental barriers arising at different times: the Kolyma Uplands, Bering Strait and portions of the Bering Isthmus. Levels of divergence varied substantially, indicating evolutionary processes spanning deep and shallow time‐scales. The different demographics among taxa reflect their distinct ecological responses. SDMs predicted regional distributional changes through time and different spatial responses among taxa.

Main conclusions

Beringia predominantly constituted a dispersal corridor during the early Quaternary and a major centre of endemism in the late Quaternary. Coincident with severe glacial cycles, small mammal species were ‘caught’ in Beringia and diversified over multiple climatic phases. Relative genetic differentiation across Beringia appears to be related to ecological differences reflecting a gradual adaptation to Beringian environments through time. Some methodological constraints associated with resolving recent (late Quaternary) isolation events or drawing inferences from a single locus are discussed.     

Methods in Vicariance Biogeography: Assessment of the Implementations of Assumptions 0, 1, and 2

As we have argued previously, for the valid derivation of general area cladograms in vicariance biogeography, two requirements should be met. First, sets of area cladograms derived under assumptions 0, 1 and 2 should be inclusive (requirement I). Second, general area cladograms should be based on area cladograms, for different monophyletic groups, derived under the same assumption (requirement II). We now assess for their actual implementation of assumptions A0, A1, and A2 and for the extent to which they meet requirements I and II, the following methods (and correlated computer programs): Component Compatibility Analysis (CAFCA), Brooks Parsimony Analysis (PAUP), Component Analysis (Component 1.5), Reconciled Tree Analysis (Component 2.0), and Three Area Statement Analysis (TAS). For this purpose we use empirical ( Heterandria, Xiphophorus, Cyttaria, Eriococcus/Madarococcus ) and theoretical data sets. All programs appear to violate, to a different degree, requirement I (deriving inclusive sets of area cladograms under assumptions) when dealing with sympatric taxa under A1 or A2. Dealing with sympatric taxa a posteriori only prevents this violation. All programs examined appear to meet requirement II (deriving general area cladograms under a single assumption).     

Conservation genetics and species status of an endangered Australian dragon, <Emphasis Type="Italic">Tympanocryptis pinguicolla</Emphasis> (Reptilia: Agamidae)

We present a phylogenetic and morphological study of the grassland earless dragon, Tympanocryptis pinguicolla, an endangered habitat specialist that occurs in a few isolated populations in eastern Australia. Tympanocryptis pinguicolla occurred historically in Victoria in south-eastern Australia, but has not been seen since 1990, and current populations are known in New South Wales and Canberra in south-eastern Australia. Recently, new populations identified as T. pinguicolla were discovered on the Darling Downs, Queensland. Translocation of individuals between these populations has been suggested as a conservation management strategy to maintain genetic diversity. To address this issue, we undertook a phylogenetic study of all major populations of T. pinguicolla using a 1838 bp region of mitochondrial DNA, incorporating ND1, ND2, COI and eight tRNA genes. We incorporated specialized degraded-DNA techniques to amplify DNA from historical museum specimens, as no extant tissue was available for Victorian populations. Our results, which include morphological analysis, provide convincing evidence that populations currently identified as T.␣pinguicolla do not comprise a monophyletic species, as the populations from the Darling Downs are more closely related to T. tetraporophora than to T. pinguicolla. In addition, we find that there is a significant level of haplotype divergence between populations of T. pinguicolla, indicating that these lineages separated at least 1.5 mya. Our results suggest translocation may not be an appropriate management strategy and our findings that Darling Downs populations are not T.␣pinguicolla will significantly influence the conservation management of this species in Queensland.     

Molecular phylogeny of caprines (Bovidae, Antilopinae): the question of their origin and diversification during the Miocene

Caprines include all bovids related to sheep and goat. The composition of the group is controversial and inter-generic relationships have been widely debated. Here, we analysed 2469 characters draw from three distinct molecular markers, i.e. two mitochondrial genes (cytochrome b and 12S rRNA) and one nuclear fragment (exon 4 of the κ -casein gene). The taxonomic sampling includes all genera putatively described as caprines, as well as several other bovid genera in order to elucidate the position of caprines within the family Bovidae, and to determine the exact composition of the group. Phylogenetic analyses confirm firstly that Pseudoryx and Saiga do not belong to caprines, and secondly, that all tribes classically defined in the literature are not monophyletic, supporting the inclusion of all caprine species into a unique enlarged tribe Caprini sensu lato . Our results are in contradiction with previous investigations suggesting a sister-group relationship between Ovis (sheep and mouflons) and Budorcas (takins). By using a molecular calibration point at 18.5 Mya for the first appearance of bovids, we estimated divergence times with our molecular data. We also performed biogeographic inferences to better understand the origin and diversification of caprines during the Neogene. Our analyses suggest that caprines shared a common ancestor with Alcelaphini and Hippotragini in the middle-late Miocene (13.37 ± 0.70 Mya). Our results also indicate that the extant generic diversity of caprines resulted from a rapid adaptive radiation during the late Miocene, at 10.96 ± 0.73 Mya. We propose that this adaptive radiation resulted from the acquisition of reduced metacarpals, a key innovation which occurred during the late Miocene as a consequence of insularity isolation in the mountainous mega-archipelago between Mediterranean and Paratethys Seas.