Origins of Bradyrhizobium nodule symbionts from two legume trees in the Philippines

Aim Geographic affinities were analysed for nodule bacteria (Bradyrhizobium sp. Jordan) associated with two legume trees indigenous to the Philippines: Pterocarpus indicus (Papilionoideae) and Wallaceodendron celebicum (Mimosoideae). Location Nodule bacteria from Luzon, the Philippines, were compared with reference strains from Central America, eastern North America, Japan, Korea, China and Australia. Methods Two PCR assays targetting length polymorphisms in the rRNA region were carried out on 96 Philippine bacterial isolates. A 496‐bp portion of the 23S rRNA gene was sequenced in 14 representative isolates. Eight strains were analysed in greater depth by sequencing portions of four other genes (16S rRNA [1410 bp], dnaK [603 bp], nifD [822 bp], recA [512 bp]), and phylogenetic trees were constructed by maximum parsimony, neighbour joining and maximum likelihood methods. Results Most of the Philippine Bradyrhizobium strains showed greater similarity to reference strains from Central America than to strains from other source regions included in the analysis. However, phylogenetic trees for the five genes had significantly conflicting topologies, suggesting that lateral gene transfer events had altered genealogical relationships at different loci. In particular, two Philippine strains resembled Bradyrhizobium strains from Central America or China for 16S rRNA, dnaK and recA sequences, but had nifD sequences that clustered with Australian strains (with bootstrap support values of 90–96%). Main conclusions The Philippines have been colonized by Bradyrhizobium strains from multiple source regions. Subsequent lateral gene transfer has resulted in the evolution of Bradyrhizobium strains that combine DNA segments of different geographic origin.     

Forgotten in the ocean: systematics,biogeography and evolution of the Trachylepis skinks of the Socotra Archipelago

Sindaco, R., Metallinou, M., Pupin, F., Fasola, M. & Carranza, S. (2012). Forgotten in the ocean: systematics, biogeography and evolution of the Trachylepis skinks of the Socotra Archipelago. —Zoologica Scripta, 41, 346–362. The Socotra Archipelago, in the north‐west Indian Ocean, is considered to be one of the most remote and most biodiversity rich and distinct islands in the world. Often referred to as the ‘Galapagos of the Indian Ocean’, it was designated a UNESCO World Heritage Natural site in 2008. Despite having a very rich and bizarre fauna and flora with a high level of endemicity at both species and generic levels, the taxonomy of most of the groups is still not clear, and their origin and evolution remain unknown. Reptiles constitute the most relevant vertebrate fauna of the Socotra Archipelago, with 90% of the 30 species and 45% of the 12 genera being found nowhere else in the world. The skinks of the endemic species Trachylepis socotrana are the only reptile species in the Archipelago distributed across all four islands (Socotra, Darsa, Samha and Abd Al Kuri). Although the species is very well known from Socotra Island, it was not discovered on Samha until 1999 and on Darsa until 2000, whereas only a few citations and one single Museum specimen exist for the population from Abd Al Kuri. To clarify the systematics, biogeography and evolution of Trachylepis socotrana, we assembled a dataset for Mabuya sensu lato including 904 base pairs (bp) of sequence (392 bp from the 12S and 512 from the 16S rRNA mitochondrial genes) for 115 individuals, including specimens of T. socotrana from all four island populations, numerous representatives of the genus Trachylepis from the Middle East, Africa and Madagascar, plus some individuals from each of the other three genera of Mabuya sensu lato (Chioninia, Eutropis and Mabuya). The results of the phylogenetic analyses indicate that, contrary to what was previously thought, members of the genus Trachylepis have colonized the Socotra Archipelago in two independent events, with the first giving rise to the populations from Socotra, Samha and Darsa and the second to the Trachylepis from Abd Al Kuri Island. According to the calibrations, both colonization events occurred within the last fourteen million years, when the Socotra Archipelago had already drifted away from Arabia, thus ruling out vicariance. Both morphological and genetic data show that the Trachylepis from Abd Al Kuri is a distinct taxon, which is herein described as a new species belonging to the T. brevicollis species complex. On the basis of this evidence, the terrestrial herpetofauna from Abd Al Kuri is composed exclusively of endemic species (one of which, the gecko Pristurus abdelkuri, was introduced into some parts of Socotra).     

Mid-Holocene and glacial-maximum vegetation geography of the northern continents and Africa

BIOME 6000 is an international project to map vegetation globally at mid‐Holocene (6000 ¹⁴C yr bp ) and last glacial maximum (LGM, 18,000 ¹⁴C yr bp ), with a view to evaluating coupled climate‐biosphere model results. Primary palaeoecological data are assigned to biomes using an explicit algorithm based on plant functional types. This paper introduces the second Special Feature on BIOME 6000. Site‐based global biome maps are shown with data from North America, Eurasia (except South and Southeast Asia) and Africa at both time periods. A map based on surface samples shows the method’s skill in reconstructing present‐day biomes. Cold and dry conditions at LGM favoured extensive tundra and steppe. These biomes intergraded in northern Eurasia. Northern hemisphere forest biomes were displaced southward. Boreal evergreen forests (taiga) and temperate deciduous forests were fragmented, while European and East Asian steppes were greatly extended. Tropical moist forests (i.e. tropical rain forest and tropical seasonal forest) in Africa were reduced. In south‐western North America, desert and steppe were replaced by open conifer woodland, opposite to the general arid trend but consistent with modelled southward displacement of the jet stream. The Arctic forest limit was shifted slighly north at 6000 ¹⁴C yr bp in some sectors, but not in all. Northern temperate forest zones were generally shifted greater distances north. Warmer winters as well as summers in several regions are required to explain these shifts. Temperate deciduous forests in Europe were greatly extended, into the Mediterranean region as well as to the north. Steppe encroached on forest biomes in interior North America, but not in central Asia. Enhanced monsoons extended forest biomes in China inland and Sahelian vegetation into the Sahara while the African tropical rain forest was also reduced, consistent with a modelled northward shift of the ITCZ and a more seasonal climate in the equatorial zone. Palaeobiome maps show the outcome of separate, independent migrations of plant taxa in response to climate change. The average composition of biomes at LGM was often markedly different from today. Refugia for the temperate deciduous and tropical rain forest biomes may have existed offshore at LGM, but their characteristic taxa also persisted as components of other biomes. Examples include temperate deciduous trees that survived in cool mixed forest in eastern Europe, and tropical evergreen trees that survived in tropical seasonal forest in Africa. The sequence of biome shifts during a glacial‐interglacial cycle may help account for some disjunct distributions of plant taxa. For example, the now‐arid Saharan mountains may have linked Mediterranean and African tropical montane floras during enhanced monsoon regimes. Major changes in physical land‐surface conditions, shown by the palaeobiome data, have implications for the global climate. The data can be used directly to evaluate the output of coupled atmosphere‐biosphere models. The data could also be objectively generalized to yield realistic gridded land‐surface maps, for use in sensitivity experiments with atmospheric models. Recent analyses of vegetation‐climate feedbacks have focused on the hypothesized positive feedback effects of climate‐induced vegetation changes in the Sahara/Sahel region and the Arctic during the mid‐Holocene. However, a far wider spectrum of interactions potentially exists and could be investigated, using these data, both for 6000 ¹⁴C yr bp and for the LGM.     

Molecular phylogeny and historical biogeography of the genus Tuber, the 'true truffles'

Aim Various data sets and methods of analysis were combined to produce the first comprehensive molecular phylogeny of the genus Tuber and to analyse its biogeography. Location Europe, North Africa, China, Asia, North America. Methods Phylogenetic relationships among Tuber species were reconstructed based on a data set of internal‐transcribed spacer (ITS) sequences and various phylogenetic inference methods, specifically maximum parsimony, Bayesian analysis and neighbour joining. Tajima’s relative rate test showed that Tuber 18S rRNA, 5.8S rRNA, 5.8S‐ITS2 rRNA and β‐tubulin sequences evolved in a clock‐like manner. These genes, combined or not, were employed for molecular clock estimates after construction of linearized trees using mega 3.1. We reconstructed ancestral areas in the Northern Hemisphere by means of a dispersal–vicariance analysis (diva 1.1) based on current distribution patterns of the genus Tuber determined from the literature. Results The resulting molecular phylogeny divided the genus Tuber into five distinct clades, in agreement with our previously published studies. The Puberulum, Melanosporum and Rufum groups were diversified in terms of species and geographical distribution. In contrast, the Aestivum and Excavatum groups were less diversified and were located only in Europe or North Africa. Using a global molecular clock analysis, we estimated the divergence times for the origin of the genus and for the origin of several groups. diva inferred nine dispersal events and suggested that the ancestor of Tuber was originally present in Europe or was widespread in Eurasia. Equally optimal distributions were obtained for several nodes, suggesting different possible biogeographical patterns. Main conclusions Our analyses identified several discrepancies with the classical taxonomy of the genus, and we propose a new phylogenetic classification. According to molecular clocks, the radiation of the genus Tuber could have started between 271 and 140 Ma. Used in combination with the results obtained from time divergence estimates, this allows us to propose two equally probable scenarios of intra‐ and inter‐continental diversification of the genus according to the geographic distribution of the most recent common ancestor in Europe or Eurasia. The biogeographical patterns imply intra‐continental dispersal events between Europe and Asia and inter‐continental dispersal events between North America and Europe or Asia, which are compatible with land connections during the Tertiary.     

Phylogeny and biogeography of tropical carnivorous land‐snails (Pulmonata: Streptaxoidea) with particular reference to East Africa and the Indian Ocean

Rowson, B., Tattersfield, P. & Symondson, W. O. C. (2010). Phylogeny and biogeography of tropical carnivorous land‐snails (Pulmonata: Streptaxoidea) with particular reference to East Africa and the Indian Ocean. —Zoologica Scripta, 40, 85–98. A phylogeny is presented for the speciose, near pan‐tropical, carnivorous achatinoid land‐snail superfamily Streptaxoidea inferred from DNA sequences (two nuclear and two mitochondrial regions) from 114 taxa from Africa, the Indian Ocean, Asia, South America and Europe. In all analyses, Streptaxidae are monophyletic, while the (two to six) previously recognised subfamilies are polyphyletic, as are several genus‐level taxa including the most speciose genus Gulella, necessitating major taxonomic review. The Asian Diapheridae are sister to Streptaxidae, which forms several well‐supported clades originating in a persistent basal polytomy. Divergence dating estimates, historical biogeography, and the fossil context suggest a Cretaceous origin of these families, but suggest Gondwanan vicariance predated most radiation. The basal polytomy dates to the Paleogene and may correspond to a rapid radiation in Africa. There is evidence for multiple Cenozoic dispersals followed by radiation, including at least two from Africa to South America, at least two from Africa to Asia and at least two from Africa to Madagascar, indicating Cenozoic turnover in tropical snail faunas. The endemic Seychelles and Mascarene streptaxid faunas each are composites of early Cenozoic lineages and more recent dispersals from Africa, with no direct evidence for an Asian origin as currently proposed. Peak streptaxid diversity in East Africa is explained by Neogene speciation among a large number of coexisting ancient lineages, a phenomenon most pronounced in the Eastern Arc‐Coastal Forests centre of endemism. This includes Miocene diversification in Gulella, a primarily East and South‐East African group which remains strikingly diverse even after unrelated ‘Gulella’ species are reclassified.     

An integrative approach to the evolution of shrimps of the genus Palaemon (Decapoda,Palaemonidae)

Shrimps of the genus Palaemon Weber, 1795 comprise of 86 species with a wide morphological and ecological variability along the tropical and temperate regions. Studies based on molecular data have indicated that despite a recent taxonomic rearrangement, it may remain not monophyletic. On the other hand, cladistic, morphological analyses have suggested the presence of synapomorphies, implying a natural status for the genus. In this work, a broad taxonomic and molecular sampling is applied to verify whether Palaemon is a monophyletic taxon and, based on the recovered phylogeny, identify geographical and morphological patterns related to the lineages. Partial sequences of 16S rRNA, histone H3 and 18S rRNA from 60 species of Palaemon and 15 species from other genera of Palaemonidae were analysed. In addition, previously used characters as well as novel diagnostic characters were scrutinized. The present phylogeny indicates that the species of Palaemon fall into three distinct lineages and that the colonization of America and Europe likely occurred multiple times. Morphological characters allow for the identification of at least four monophyletic groups in Palaemon; two of which are monospecific at the moment. Based on the present results, it may become necessary to establish two new genera (to accommodate Palaemon concinnus and Palaemon mercedae, respectively), as well as re‐erect the genus Alaocaris Holthuis, 1949 for Palaemon antrorum, potentially including a further six American species.     

Complete rRNA sequence, arrangement of tandem repeated units and phylogeny of Nosema fumiferanae from spruce budworm, Choristoneura fumiferana (Clemens)

We provide molecular systematics of a microporidian species, Nosema fumiferanae, one of the most common natural enemies of spruce budworm, Choristoneura fumiferana. The uncharacterized flanking region upstream of the large subunit (LSU) rRNA and the complete rRNA cistron of N. fumiferanae was 4,769 bp long. The organization of the rRNA gene was 5′‐LSU rRNA‐ITS‐SSU rRNA‐IGS‐5S‐3′ and corresponded primarily to most insect (i.e. lepidopteran) Nosema species identified and classified to date. Phylogenetic analysis based on the complete rRNA cistron indicated that N. fumiferanae is closely related to Nosema plutellae and is correctly assigned to the “true” Nosema group. Suggestions were provided on a criterion to delineate the “true” Nosema from other microsporidian species.     

Biogeography of ‘tropical Anagallis’ (Myrsinaceae) inferred from nuclear and plastid DNA sequence data

Aim ‘Tropical Anagallis’ corresponds to one of two evolutionary lineages within the genus Anagallis L. Generally, species within this lineage have a limited distribution in (sub‐)tropical regions in Africa or Madagascar. Two species, however, are endemic to South America, and exhibit a trans‐Atlantic disjunction with the rest of the species within the lineage. To investigate this disjunct distribution, as well as other dispersal events, the distribution of extant taxa was used to hypothesize the ancestral area(s) of distribution. Location Africa, Madagascar, Europe and South America. Methods Dispersal–vicariance analysis (DIVA) was used to optimize distribution areas onto parsimony and Bayesian phylogenies based on sequence data from four chloroplast loci and the nuclear internal transcribed spacers (ITS). Results Parsimony analysis gave one most parsimonious tree while Bayesian analysis resulted in a collapsed node due to alternative placements of Anagallis nummularifolia Baker, endemic to Madagascar. Optimization of the present distribution using DIVA, and the most parsimonious tree and six alternative topologies of the Bayesian analysis, show an origin of the lineage in Europe as most likely, although one topology indicates a broader ancestral distribution area. Dispersal to Africa appears to have been a single event, while two parallel dispersal events seem to have resulted in the American as well as Madagascan distributions. Main conclusions The lineage ‘tropical Anagallis’ evolved in Europe and may have been present in the Eocene boreotropical forests, although scarcity of fossils makes assessment of age difficult. Dispersal to South America is proposed to have been via the North Atlantic land bridge, or, more likely, through transport by the North Equatorial Current. Dispersal from Europe to Africa represents a single event, while dispersal to Madagascar from mainland Africa has occurred twice.     

Deconstructing the eradication of new world screwworm in North America: retrospective analysis and climate warming effects

Before its eradication from North America, the subtropical‐tropical new world screwworm fly Cochliomyia hominivorax (Coquerel) invaded southwestern temperate areas of the U.S.A., where it caused myiasis in wildlife and livestock. Outbreaks of the fly occurred during years when adult migrants were carried northward on North American monsoon winds from the northern areas of Mexico and south Texas. We deconstruct, retrospectively, the biology and the effect of weather on the eradication of the fly in North America. Screwworm was found to be an ideal candidate for eradication using the sterile insect technique (SIT) because females mate only once, whereas males are polygynous, and, although it has a high reproductive potential, field population growth rates are low in tropical areas. In northern areas, eradication was enhanced by cool‐cold weather, whereas eradication in tropical Mexico and Central America is explained by the SIT. Despite low average efficacy of SIT releases (approximately 1.7%), the added pressure of massive SIT releases reduced intrinsically low fly populations, leading to mate‐limited extinction. Non‐autochthonous cases of myiasis occur in North America and, if the fly reestablishes, climate warming by 2045–2055 will expand the area of favourability and increase the frequency and severity of outbreaks.     

The 18S and 5S ribosomal RNA genes in Oenothera mitochondria: Sequence rearrangments in the 18S and 5S rRNA genes of higher plants

Summary The 18S and 5S ribosomal RNA genes are separated by a 582-nucleotide-long spacer region in the Oenothera mitochondrial genome. The 5S rRNA gene is 7 bp shorter than the maize and 3 bp shorter than the wheat sequences due to a 4 bp deletion in a side arm of the secondary structure model. The 18S rRNA molecule can be folded analogously to the maize and wheat mitochondrial and Escherichia coli models for this rRNA. Most of the sequence variations between the wheat and Oenothera molecules are located in the variable domains identified for the wheat 18S rRNA.The comparison of the 18S rRNA from the mitochondria of Oenothera as a representative of dicotyledonous plants with that of the monocotyledons wheat and maize provides an indication of the rate of diversity in higher plant mitochondrial genes and gives direct evidence for sequence rearrangements within the 18 S rRNA genes.     

Comparative phylogeography of Amphicarpaea legumes and their root-nodule symbionts in Japan and North America

Aim Relationships of eastern Asian and eastern North American populations of legumes in the genus Amphicarpaea Elliot ex. Nuttall (Phaseoleae–Glycininae) and their root nodule bacteria (Bradyrhizobium Jordan) were analysed to test whether both organisms share an identical biogeographic history. Location Japan and eastern North America (New York and Illinois). Methods Sequences of three plant genes (chloroplast trnL region, nuclear ribosomal ITS, and histone H3‐D) and a segment of the bacterial ribosomal region (partial 16S rRNA and 23S rRNA genes, and the 16S rRNA–23S rRNA ITS) were used to analyse phylogenetic relationships. Results For plants, Japanese populations formed a sister group to a well‐supported clade of all North American genotypes. For nodule bacteria associated with Amphicarpaea, isolates from North America did not form a single clade relative to Asian genotypes. Japanese Bradyrhizobium isolates were closely related to particular sub‐groups of North American bacteria (lineages ‘B’ and ‘C’), with other American bacteria branching earlier. Main conclusions Plants and bacteria showed clear deviations from a pattern of parallel cladogenesis. The most basal Amphicarpaea lineage was associated with a recently‐diverged bacterial group, while one recently‐diverged plant lineage had symbionts that branched in a basal position relative to the other Amphicarpaea bacteria. When analysed with data on symbiotic compatibility from inoculation experiments, the molecular phylogenies suggested that for plants, at least one transition has occurred toward more promiscuous nodulation behaviour. Among bacteria, strains with narrow host range on Amphicarpaea appear to be ancestral to symbiotic generalists.     

The nucleotide sequence of the entire ribosomal DNA operon and the structure of the large subunit rRNA of Giardia muris

Summary The total nucleotide sequence of the rDNA of Giardia muris, an intestinal protozoan parasite of rodents, has been determined. The repeat unit is 7668 basepairs (bp) in size and consists of a spacer of 3314 bp, a small-subunit rRNA (SSU-rRNA) gene of 1429, and a large-subunit rRNA (LSU-rRNA) gene of 2698 bp. The spacer contains long direct repeats and is heterogeneous in size. The LSU-rRNA of G. muris was compared to that of the human intestinal parasite Giardia duodenalis, to the bird parasite Giardia ardeae, and to that of Escherichia coli. The LSU-rRNA has a size comparable to the 23S rRNA of E. coli but shows structural features typical for eukaryotes. Some variable regions are typically small and account for the overall smaller size of this rRNA. The structure of the G. muris LSU-rRNA is similar to that of the other Giardia rRNA, but each rRNA has characteristic features residing in a number of variable regions.Offprint requests to: H. van Keulen     

A host species‐informative internal control for molecular assessment of African swine fever virus infection rates in the African sylvatic cycle Ornithodoros vector

African swine fever virus (ASFV) infection in adult Ornithodoros porcinus (Murry 1877, sensu Walton 1979 ) ticks collected from warthog burrows in southern and East Africa was assessed using a duplex genomic amplification approach that is informative with respect to the invertebrate host species and infecting sylvatic cycle virus. DNA extracted from individual ticks was used as template for the simultaneous amplification of a C‐terminal 478‐bp ASFV p72 gene region and a ～313‐bp fragment of the tick mitochondrial 16S rRNA gene, under optimized reaction conditions. Within‐warthog burrow infection rates ranged from 0% to 43% using this approach, and phylogenetic analysis of 16S gene sequences revealed the presence of three geographically discrete O. porcinus lineages, but no support for subspecies recognition. False negatives are precluded by the inclusion of host species‐informative primers that ensure the DNA integrity of cytoplasmically located genome extracts. In addition, infection rate estimates are further improved as false positives arising from carry‐over contamination when performing a two‐step nested polymerase chain reaction are negated by the one‐step approach. Phylogenetic comparison of full‐length virus gene sequences with the partial C‐terminal p72 gene target confirmed the epidemiological utility of the latter in a sylvatic setting. The method is therefore of particular value in studies assessing the prevalence and diversity of ASFV in relation to the African sylvatic tick vector and holds potential for investigating the role of alternative tick species in virus maintenance and transmission.     

Early evolutionary history of the flowering plant family Annonaceae: steady diversification and boreotropical geodispersal

Aim Rain forest‐restricted plant families show disjunct distributions between the three major tropical regions: South America, Africa and Asia. Explaining these disjunctions has become an important challenge in biogeography. The pantropical plant family Annonaceae is used to test hypotheses that might explain diversification and distribution patterns in tropical biota: the museum hypothesis (low extinction leading to steady accumulation of species); and dispersal between Africa and Asia via Indian rafting versus boreotropical geodispersal. Location Tropics and boreotropics. Methods Molecular age estimates were calculated using a Bayesian approach based on 83% generic sampling representing all major lineages within the family, seven chloroplast markers and two fossil calibrations. An analysis of diversification was carried out, which included lineage‐through‐time (LTT) plots and the calculation of diversification rates for genera and major clades. Ancestral areas were reconstructed using a maximum likelihood approach that implements the dispersal–extinction–cladogenesis model. Results The LTT plots indicated a constant overall rate of diversification with low extinction rates for the family during the first 80 Ma of its existence. The highest diversification rates were inferred for several young genera such as Desmopsis, Uvariopsis and Unonopsis. A boreotropical migration route was supported over Indian rafting as the best fitting hypothesis to explain present‐day distribution patterns within the family. Main conclusions Early diversification within Annonaceae fits the hypothesis of a museum model of tropical diversification, with an overall steady increase in lineages possibly due to low extinction rates. The present‐day distribution of species within the two largest clades of Annonaceae is the result of two contrasting biogeographic histories. The ‘long‐branch clade’ has been diversifying since the beginning of the Cenozoic and underwent numerous geodispersals via the boreotropics and several more recent long‐distance dispersal events. In contrast, the ‘short‐branch clade’ dispersed once into Asia via the boreotropics during the Early Miocene and further dispersal was limited.     

Detection and Molecular Characterization of a 16SrII‐A* Phytoplasma in Grapefruit (Citrus paradisi) with Huanglongbing‐like Symptoms in China

In the year 2010, in a survey in Guangxi Province, China, to detect and characterize phytoplasmas in a huanglongbing (HLB)‐infected grapefruit (Citrus paradisi) orchard, 87 leaf samples with symptoms of blotchy mottle were collected from symptomatic grapefruit trees, and 320 leaf samples from symptomless trees adjacent to the symptomatic trees. Nested polymerase chain reaction (PCR) using universal phytoplasma primer set P1/P7 followed by primer set fU5/rU3 identified 7 (8.0%) positive samples from symptomatic samples but none from symptomless samples. Of the 87 symptomatic samples, 77 (88.5%) were positive for ‘Candidatus Liberibacter asiaticus’ and 5 for both phytoplasma and ‘Ca. L. asiaticus’. Sequence analysis indicated that seven 881‐bp amplicons, amplified by nested phytoplasma primer sets P1/P7 and fU5/rU3, shared 100.0% sequence identity with each other. Genome walking was then performed based on the 881 bp known sequences, and 5111 bp of upstream and downstream sequences were obtained. The total 5992 bp sequences contained a complete rRNA operon, composed of a 16S rRNA gene, a tRNA^Ile gene, a 23S rRNA gene and a 5S rRNA gene followed by eight tRNA genes. Phylogenetic analysis and virtual restriction fragment length polymorphism analysis confirmed the phytoplasma was a variant (16SrII‐A*) of phytoplasma subgroup 16SrII‐A. As phytoplasmas were only detected in blotchy‐mottle leaves, the 16SrII‐A* phytoplasma identified was related to HLB‐like symptoms.     

Phylogenetics and population genetics of the louse fly,Lipoptena mazamae,from Arkansas,U.S.A.

Louse flies, also known as deer keds (Lipoptena mazamae Rondani), infest cervids such as white‐tailed deer, Odocoileus virginianus and vector pathogens such as Anaplasma and Bartonella schoenbuchensis to cattle and humans, respectively. The population genetic structure of 30 L. mazamae collected from white‐tailed deer in four regions of Arkansas, U.S.A., designated by county boundaries, was examined using DNA sequences of a 259‐bp region of the mitochondrial DNA rRNA 16S gene. Of the 259 nucleotide characters, 33 were variable and 6 haplotypes were identified. Two haplotypes occurred only once (haplotype 3 and 4), whereas two other haplotypes occurred in 43% (haplotype 1 in two regions) and 40% (haplotype 6 in three regions) of the samples. Phylogenetic relationships of the six L. mazamae haplotypes were constructed with other Hippoboscid and Glossinid samples and two clades resulted. Clade 1 was located in the north and western Ozarks whereas clade 2 was found in the northern and eastern Ozarks. Results from the present study indicate that Lipoptena may be a polyphyletic genus; consequently, more research into genetic variation within this genus is necessary.     

Contrasts in the large herbivore faunas of the southern continents in the late Pleistocene and the ecological implications for human origins

Aim

Africa is renowned for the current abundance and diversity of its large mammals. The aim of this study was to assess distinctions evident in the functional composition of continental large herbivore faunas during the late Pleistocene before extinctions depleted the megafauna outside Africa.

Location

The African large herbivore fauna was compared with that formerly inhabiting South America, Australia, North America, Eurasia and tropical Asia during the late Pleistocene.

Methods

Pleistocene faunas were reconstructed from the literature in terms of their relative body size composition, grazer/browser contributions and taxonomic representations, omitting forest and island species.

Results

Although the three southern continents were closely similar in the overall species richness of large herbivores that they supported during the late Pleistocene, South America had a predominance of very large herbivores, while most of Australia's mammalian herbivores were relatively small and those of Africa were intermediate. Africa had many more grazers, especially in the size range 100–1000 kg, than other continents. The South American pattern resembled that in North America and Eurasia, while Africa and Australia diverged in different ways.

Main conclusions

Neither the total extent of savannas in each continent nor the morphological features enabling bovid radiation seemed adequate on their own to explain the greater richness of macrograzers in Africa. Africa is characterized by the widespread occurrence of arid/eutrophic savannas, which are unrepresented in other continents. The prevalence of savanna is partly attributable to the high elevation of interior eastern and southern Africa, associated with relatively low rainfall, and to the comparatively high soil fertility, related to volcanic influences. This promoted an abundance and diversity of medium‐sized grazing ruminants unrivalled elsewhere. Indigenous grasses in South America and Australia are less well adapted to withstand severe grazing than the African grasses introduced to support livestock. The locally high abundance of African ungulates presented conditions that facilitated the adaptive transition by early hominins from plant‐gatherers to meat‐scavengers.     

The butterfly Danaus chrysippus (L.) in East Africa comprises polyphyletic, sympatric lineages that are, despite behavioural isolation, driven to hybridization by female-biased sex ratios

Mitochondrial and nuclear DNA information was analysed among four subspecies of the African Queen butterfly, Danaus (Anosia) chrysippus sensu lato (s.l.), along with four other Danaus species drawn from all three subgenera (D. (Danaus) plexippus, D. (Salatura) genutia, D. (A.) gilippus, D. (A.) eresimus) and two outgroup species from the same tribe, Tirumala septentrionis and Amauris niavius. A mitochondrial phylogeny derived from the 12S rRNA (347 bp) and COI (537 bp) loci indicates two very distinct haplotypes for subspecies D. (A.) c. dorippus, dorippus‐1 and dorippus‐2. Interestingly, dorippus‐1, on the one hand, and all other D. (A.) chrysippus haplotypes, on the other, are the most distantly related clades within the genus and have different most recent ancestors from different subgenera, though sharing the common ancestor of the monophyletic genus. A phylogeny based on the EF1‐α nuclear locus (400 bp) shows that the two well‐separated mitochondrial lineages of dorippus are identical for this gene and reciprocally monophyletic to the other D. (A.) chrysippus lineages. Thus, nuclear and cytoplasmic phylogenies are not only discordant, but also suggest that both D. (A.) chrysippus s.l. and subspecies dorippus are polyphyletic. Paradoxically, four African subspecies, chrysippus‐orange, chrysippus‐brown, alcippus and dorippus, though substantially vicariant, hybridize extensively in East Africa wherever the ranges of two or more of them overlap. Linkage disequilibrium, and hence sexual isolation, in sympatry between colour (nuclear) genes and unlinked mitochondrial (cytoplasmic) loci is consistent across populations and therefore indicates the operation of positive natural selection. Together with data from previous experimental and field work, our results suggest that extensive hybridization occurs among once allopatric or parapatric lineages, that are now nascent species. We deduce that hybridism among lineages in sympatry is currently enforced, in the face of assortative mate choice, by a bacterial symbiont, Spiroplasma, a male‐killer that forces females in female‐biased populations to pair with heterotypic males. In discussion we emphasize that neither D. (A.) chrysippus s.l. as presently circumscribed, nor its component clades, conform to any established concept of species. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 86 , 117–131.     

Fig trees at the northern limit of their range: the distributions of cryptic pollinators indicate multiple glacial refugia

Climatic oscillations during the last few million years had well‐documented effects on the distributions and genomes of temperate plants and animals, but much less is known of their impacts on tropical and subtropical species. In contrast to Europe and North America, ice‐sheets did not cover most of China during glacial periods, and the effects of glacial cycles were less dramatic. Fig trees are a predominantly tropical group pollinated by host‐specific fig wasps. We employed partial mitochondrial COI (918 bp) and nuclear ITS2 (462 bp) gene sequences to investigate the genetic structure and demographic histories of the wasps that pollinate the subtropical Ficus pumila var. pumila in Southeastern China. Deep genetic divergence in both mitochondrial (7.2–11.6%) and nuclear genes (1.6–2.9%) indicates that three pollinator species are present and that they diverged about 4.72 and 6.00 Myr bp . This predates the Quaternary ice ages, but corresponds with the formation of the Taiwan Strait and uplifting of the Wuyi–Xianxia Mountains. The three pollinators have largely allopatric distribution patterns in China and display different postglacial demographic histories. Wiebesia spp. 1 and 2 occupy, respectively, the northern and southern regions of the mainland host range. Their populations both underwent significant postglacial spatial expansions, but at different times and at different rates. Wiebesia sp. 3 is largely restricted to northern islands and shows less evidence of recent population expansion. Their mainly allopatric distributions and different demographic histories are consistent with host plant postglacial expansion from three distinct refugia and suggest one mechanism whereby fig trees gain multiple pollinators.