An Assessment of the Systematics of Arvicanthine Rodents Using Mitochondrial DNA Sequences: Evolutionary and Biogeographical Implications

Mitochondrial DNA sequences of cytochrome b (1140-bp), 12S (375-bp) and 16S (475-bp) ribosomal RNA gene fragments were used to investigate the phylogenetic relationships of a group of African rodents referred as the arvicanthines (Family Muridae, Subfamily Murinae). A total of 49 specimens including all seven genera and 15 of the 24 arvicanthine species currently recognized as well as outgroups from the subfamily Acomyinae, Arvicolinae, Gerbillinae, Murinae and Otomyinae were examined. Our molecular data support the monophyly of the African arvicanthine genera and their partition into three distinct lineages: one composed of Arvicanthis, Mylomys and Pelomys, one composed of Desmomys and Rhabdomys, and one represented by Lemniscomys. The Indian arvicanthine Golunda is external to this clade and is part of a larger clade, together with the African arvicanthines and other African Murinae such as Aethomys, Dasymys, Grammomys, and Hybomys, for which we propose the use of the tribal name Arvicanthini. The basal relationships within this set of species are poorly resolved, suggesting the possibility of a rapid radiation. Calibration based on the fossil record suggests that this radiative event would have taken place at about 8.0 Mya (Million years ago). The identification of the Otomyinae as the sister-taxon to Arvicanthini implies that the former are true murines and should therefore be given only tribal rank within the Murinae.     

The pattern and timing of diversification of Philippine endemic rodents: evidence from mitochondrial and nuclear gene sequences

The 22 genera and 64 species of rodents (Muridae: Murinae) distributed in the Philippine Islands provide a unique opportunity to study patterns and processes of diversification in island systems. Over 90% of these rodent species are endemic to the archipelago, but the relative importance of dispersal from the mainland, dispersal within the archipelago, and in situ differentiation as explanations of this diversity remains unclear, as no phylogenetic hypothesis for these species and relevant mainland forms is currently available. Here we report the results of phylogenetic analyses of the endemic Philippine murines and a wide sampling of murine diversity from outside the archipelago, based on the mitochondrial cytochrome b gene and the nuclear-encoded IRBP exon 1. Analysis of our combined gene data set consistently identified five clades comprising endemic Philippine genera, suggesting multiple invasions of the archipelago. Molecular dating analyses using parametric and semiparametric methods suggest that colonization occurred in at least two stages, one ca. 15 Mya, and another 8 to 12 million years later, consistent with the previous recognition of "Old" and "New" endemic rodent faunas. Ancestral area analysis suggests that the Old Endemics invaded landmasses that are now part of the island of Luzon, whereas the three New Endemic clades may have colonized through either Mindanao, Luzon, or both. Further, our results suggest that most of the diversification of Philippine murines took place within the archipelago. Despite heterogeneity between nuclear and mitochondrial genes in most model parameters, combined analysis of the two data sets using both parsimony and likelihood increased phylogenetic resolution; however, the effect of data combination on support for resolved nodes was method dependent. In contrast, our results suggest that combination of mitochondrial and nuclear data to estimate relatively ancient divergence times can severely compromise those estimates, even when specific methods that account for rate heterogeneity among genes are employed. [Biogeography; divergence date estimation; mitochondrial DNA; molecular systematics; Murinae; nuclear exon; Philippines; phylogeny.].     

Evolutionary history of Gymnocarpos (Caryophyllaceae) in the arid regions from North Africa to Central Asia

Gymnocarpos has only about ten species distributed in the arid regions of Asia and Africa, but it exhibits a geographical disjunction between eastern Central Asia and western North Africa and Minor Asia. We sampled eight species of the genus and sequenced two chloroplast regions (rps16 and psbB–psbH), and the nuclear rDNA (ITS) to study the phylogeny and biogeography. The results of the phylogenetic analyses corroborated that Gymnocarpos is monophyletic, in the phylogenetic tree two well supported clades are recognized: clade 1 includes Gymnocarpos sclerocephalus and G. decandrus, mainly the North African group, whereas clade 2 comprises the remaining species, mainly in the Southern Arabian Peninsula. Molecular dating analysis revealed that the divergence age of Gymnocarpos was c. 31.33 Mya near the Eocene and Oligocene transition boundary, the initial diversification within Gymnocarpos dated to c. 6.69 Mya in the late Miocene, and the intraspecific diversification mostly occurred during the Quaternary climate oscillations. Ancestral area reconstruction suggested that the Southern Arabian Peninsula was the ancestral area for Gymnocarpos. Our conclusions revealed that the aridification since mid‐late Miocene significantly affected the diversification of the genus in these areas.     

Genetics of the ceramide/sphingosine-1-phosphate rheostat in blood pressure regulation and hypertension

Background

South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present.

Results

To this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven Rattus rattus and five Rattus norvegicus haplotypes in south Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. Rattus norvegicus and R. rattus each occurred sympatrically with Rattus tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by R. tanezumi in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species.

Conclusions

This study has highlighted the value of genetic typing for detecting cryptic invasive species, providing historical insights into introductions and for directing future sampling. The apparent ease with which a cryptic species can become established signals the need for broader implementation of genetic monitoring programmes. In addition to providing baseline data and potentially identifying high-risk introduction routes, the predictive power of ecological niche modelling is enhanced when species records are genetically verified.     

Multigene phylogeny of the Old World mice, Murinae, reveals distinct geographic lineages and the declining utility of mitochondrial genes compared to nuclear genes

Despite its great diversity and biomedical importance, the rodent subfamily Murinae is poorly resolved phylogenetically. We present the first cladistic analysis sampling multiple representatives of most major groups based on DNA sequence for three nuclear (GHR, RAG1, and AP5) and one mitochondrial (COII and parts of COI and ATPase 8) fragments. Analyzed separately, the four partitions agree broadly with each other and the combined analysis. The basal split is between a clade of Philippine Old Endemics and all remaining murines. Within the latter, rapid radiation led to at least seven geographically distinct lineages, including a Southeast Asian Rattus clade; a diverse Australo-Papuan and Philippine clade; an African arvicanthine group including the otomyines; an African Praomys group; and three independent genera from Africa and Asia, Mus, Apodemus, and Malacomys. The murines appear to have originated in Southeast Asia and then rapidly expanded across all of the Old World. Both nuclear exons provide robust support at all levels. In contrast, the bootstrap proportions from mitochondrial data decline rapidly with increasing depth in the tree, together suggesting that nuclear genes may be more useful even for relatively recent divergences (< 10MYA).     

Comparison of Visceral Leishmaniasis Diagnostic Antigens in African and Asian Leishmania donovani Reveals Extensive Diversity and Region-specific Polymorphisms

Background

Visceral leishmaniasis (VL), caused by infection with Leishmania donovani complex, remains a major public health problem in endemic regions of South Asia, East Africa, and Brazil. If untreated, symptomatic VL is usually fatal. Rapid field diagnosis relies principally on demonstration of anti-Leishmania antibodies in clinically suspect cases. The rK39 immunochromatographic rapid diagnostic test (RDT) is based on rK39, encoded by a fragment of a kinesin-related gene derived from a Brazilian L. chagasi, now recognised as L. infantum, originating from Europe. Despite its reliability in South Asia, the rK39 test is reported to have lower sensitivity in East Africa. A reason for this differential response may reside in the molecular diversity of the rK39 homologous sequences among East African L. donovani strains.

Methodology/Principal Findings

Coding sequences of rK39 homologues from East African L. donovani strains were amplified from genomic DNA, analysed for diversity from the rK39 sequence, and compared to South Asian sequences. East African sequences were revealed to display significant diversity from rK39. Most coding changes in the 5′ half of repeats were non-conservative, with multiple substitutions involving charge changes, whereas amino acid substitutions in the 3′ half of repeats were conservative. Specific polymorphisms were found between South Asian and East African strains. Diversity of HASPB1 and HASPB2 gene repeat sequences, used to flank sequences of a kinesin homologue in the synthetic antigen rK28 designed to reduce variable RDT performance, was also investigated. Non-canonical combination repeat arrangements were revealed for HASPB1 and HASPB2 gene products in strains producing unpredicted size amplicons.

Conclusions/Significance

We demonstrate that there is extensive kinesin genetic diversity among strains in East Africa and between East Africa and South Asia, with ample scope for influencing performance of rK39 diagnostic assays. We also show the importance of targeted comparative genomics in guiding optimisation of recombinant/synthetic diagnostic antigens.     

Phytogeographical Implication of Bridelia Will. (Phyllanthaceae) Fossil Leaf from the Late Oligocene of India

Background

The family Phyllanthaceae has a predominantly pantropical distribution. Of its several genera, Bridelia Willd. is of a special interest because it has disjunct equally distributed species in Africa and tropical Asia i.e. 18–20 species in Africa-Madagascar (all endemic) and 18 species in tropical Asia (some shared with Australia). On the basis of molecular phylogenetic study on Bridelia, it has been suggested that the genus evolved in Southeast Asia around 33±5 Ma, while speciation and migration to other parts of the world occurred at 10±2 Ma. Fossil records of Bridelia are equally important to support the molecular phylogenetic studies and plate tectonic models.

Results

We describe a new fossil leaf of Bridelia from the late Oligocene (Chattian, 28.4–23 Ma) sediments of Assam, India. The detailed venation pattern of the fossil suggests its affinities with the extant B. ovata, B. retusa and B. stipularis. Based on the present fossil evidence and the known fossil records of Bridelia from the Tertiary sediments of Nepal and India, we infer that the genus evolved in India during the late Oligocene (Chattian, 28.4–23 Ma) and speciation occurred during the Miocene. The stem lineage of the genus migrated to Africa via “Iranian route” and again speciosed in Africa-Madagascar during the late Neogene resulting in the emergence of African endemic clades. Similarly, the genus also migrated to Southeast Asia via Myanmar after the complete suturing of Indian and Eurasian plates. The emergence and speciation of the genus in Asia and Africa is the result of climate change during the Cenozoic.

Conclusions

On the basis of present and known fossil records of Bridelia, we have concluded that the genus evolved during the late Oligocene in northeast India. During the Neogene, the genus diversified and migrated to Southeast Asia via Myanmar and Africa via “Iranian Route”.     

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.     

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

Background

Recent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia by anatomically modern humans. Further understanding requires a deeper insight into the topology of the branches of the Indian mtDNA phylogenetic tree, which should be contextualized within the phylogeography of the neighboring regional mtDNA variation. Accordingly, we have analyzed mtDNA control and coding region variation in 796 Indian (including both tribal and caste populations from different parts of India) and 436 Iranian mtDNAs. The results were integrated and analyzed together with published data from South, Southeast Asia and West Eurasia.

Results

Four new Indian-specific haplogroup M sub-clades were defined. These, in combination with two previously described haplogroups, encompass approximately one third of the haplogroup M mtDNAs in India. Their phylogeography and spread among different linguistic phyla and social strata was investigated in detail. Furthermore, the analysis of the Iranian mtDNA pool revealed patterns of limited reciprocal gene flow between Iran and the Indian sub-continent and allowed the identification of different assemblies of shared mtDNA sub-clades.

Conclusions

Since the initial peopling of South and West Asia by anatomically modern humans, when this region may well have provided the initial settlers who colonized much of the rest of Eurasia, the gene flow in and out of India of the maternally transmitted mtDNA has been surprisingly limited. Specifically, our analysis of the mtDNA haplogroups, which are shared between Indian and Iranian populations and exhibit coalescence ages corresponding to around the early Upper Paleolithic, indicates that they are present in India largely as Indian-specific sub-lineages. In contrast, other ancient Indian-specific variants of M and R are very rare outside the sub-continent.     

Melastomeae come full circle: biogeographic reconstruction and molecular clock dating

Rhexia, with 11 species in the Coastal Plain province of North America, is the only temperate zone endemic of the tropical eudicot family Melastomataceae. It is a member of the only pantropical tribe of that family, Melastomeae. Based on the chloroplast gene ndhF, we use a fossil-calibrated molecular clock to address the question of the geographic origin and age of Rhexia. Sequences from 37 species in 21 genera representing the tribe's geographical range were analyzed together with five outgroups. To obtain better clade support, another chloroplast region, the rpl16 intron, was added for 24 of the species. Parsimony analysis of the combined data and maximum-likelihood analysis of ndhF alone indicate that the deepest split is between Rhexia plus its sister group, a small Central American genus, and all other Melastomeae. Old World Melastomeae are monophyletic and nested within New World Melastomeae. Although likelihood-ratio tests of clock and nonclock substitution models for the full or moderately pruned datasets rejected the clock, these models yielded identical topologies (for 30 taxa) with few significantly different branch lengths as assessed by a Student's t-test. Age estimates obtained were 22 million years ago (Mya) for the divergence of Rhexia from its sister group, 12 Mya for the dispersal of Melastomeae from the New World to West Africa, and 1 Mya for the diversification of Melastoma in Southeast Asia. The only other genus of Melastomeae to have reached Southeast Asia from Africa or Madagascar is Osbeckia. The age and geographic distribution of fossils, which come from Miocene sites throughout Eurasia, suggest that Melastomeae once ranged from Eurasia across Beringia to North America from whence they reached South America and subsequently Africa and Southeast Asia. Climate deterioration led to their extinction in the Northern Hemisphere, with Rhexia possibly surviving in Coastal Plain refugia.     

Neogene paleobiogeography and East African paleoenvironments: contributions from the Tugen Hills rodents and lagomorphs.

A minimum of 28 genera of rodents and one genus of lagomorph were recovered from the Tugen Hills, Baringo District, Kenya, from localities dating from over 15.5 to about 4.4 Ma. The middle Miocene (sites dated between 15.8 and 15.3 Ma) rodent fauna recovered primarily from the Kipsaramon site complex, Muruyur Formation, includes a mixture of characteristically early Miocene taxa, and more derived forms. Composition of the African rodent fauna changes dramatically with the introduction of myocricetodontines, democricetodontines, and dendromurines, immigrants primarily from southern Asia. In the Tugen Hills, these taxa are first found in the Kabasero localities, Ngorora Formation, at sites dating from 12.5-12.33 Ma. A second major change in the African rodent fauna reflects the introduction of murines, immigrants from southern Asia. In the Tugen Hills murines are first encountered at Kapcheberek, Lukeino Formation, dated to 5.9-5.7 Ma. One rodent genus from the Lukeino Formation (Arvicanthis), and two from the Tabarin locality, Chemeron Formation (Heliosciurus, Paraxerus; 4.5-4.4 Ma), represent the earliest records of these extant African genera. A cricetomyine from the Ngorora Formation (12.5 Ma) is likely the earliest report of this exclusively African group. One of the earliest African records of porcupines (Hystricide) is from the Lukeino Formation. Lagomorphs are poorly represented, but include one of the earliest African occurrences of the family Leporidae from the Mpesida Beds (bracketed by dates of 7-6.2 Ma), and possibly a new genus of leporid from the Kapcheberek locality. Analysis of the Tugen Hills small mammals in association with other African records suggests several episodes of dispersal between Africa and Eurasia during the middle and late Miocene. Rodents from Kipsaramon are indicative of forests in conjunction with more open habitats. Those from the Kapcheberek locality are suggestive of a savanna habitat. The rodents from the Tabarin locality suggest a woodland environment.     

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.     

Placing the origin of two species-rich genera in the late cretaceous with later species divergence in the tertiary: a phylogenetic, biogeographic and molecular dating analysis of Piper and Peperomia (Piperaceae)

Nearly all of the species diversity in Piperaceae is encompassed within Piper and Peperomia. Both genera are pan-tropical with areas of diversification in the Neotropics and Southeast Asia. Piperaceae are less diverse in Africa with only two native species of Piper. This study examines the distribution of both Piper and Peperomia with representative samples from the Neotropics, Asia, Pacific Islands, and Africa. Molecular dating is used to place an age for the crown clades of Piper and Peperomia as well as ages for diversification within the clades. Both genera have origins in the late Cretaceous, but species level diversification occurred much later in the Tertiary. Biogeography of both genera are correlated with paleoclimate evidence to better explain the distribution and diversification of these large genera.     

African origin and global distribution patterns: Evidence inferred from phylogenetic and biogeographical analyses of ectomycorrhizal fungal genus Strobilomyces

Aim

The ectomycorrhizal genus Strobilomyces is widely distributed throughout many parts of the world, but its origin, divergence and distribution patterns remain largely unresolved. In this study, we aim to explore the species diversity, distribution and evolutionary patterns of Strobilomyces on a global scale by establishing a general phylogenetic framework with extensive sampling.

Location

Africa, Australasia, East Asia, Europe, North America, Central America and Southeast Asia.

Methods

The genealogical concordance phylogenetic species recognition method was used to delimit phylogenetic species. Divergence times were estimated using a Bayesian uncorrelated lognormal relaxed molecular clock. The ancestral area and host of Strobilomyces were inferred via the programs rasp and mesquite . The change of diversification rate over time was estimated using Ape, Laser and Bammtools software packages.

Results

We recognize a novel African clade and 49 phylogenetic species with morphological evidence, including 18 new phylogenetic species and 23 previously described ones. Strobilomyces probably originated in Africa, in association with Detarioideae/Phyllanthaceae/Monotoideae during the early Eocene. The dispersal to Southeast Asia can be explained by Wolfe's “Boreotropical migration” hypothesis. East Asia, Australasia, Europe and North/Central America are primarily the recipients of immigrant taxa during the Oligocene or later. A rapid radiation implied by one diversification shift was inferred within Strobilomyces during the Miocene.

Main conclusions

An unexpected phylogenetic species diversity within Strobilomyces was uncovered. The highest diversity, resulting probably from a rapid radiation, was found in East Asia. Dispersal played an important role in the current distribution pattern of Strobilomyces. The Palaeotropical disjunction is explained by species dispersal from Africa to Southeast Asia through boreotropical forests during the early Eocene. Species from the Northern Hemisphere and Australasia are largely derived from immigrant ancestors from Southeast Asia.     

An extensive analysis of the African rice genetic diversity through a global genotyping

Key message

We present here the first curated collection of wild and cultivated African rice species. For that, we designed specific SNPs and were able to structure these very low diverse species.

Abstract

Oryza glaberrima, the cultivated African rice, is endemic from Africa. This species and its direct ancestor, O. barthii, are valuable tool for improvement of Asian rice O. sativa in terms of abiotic and biotic stress resistance. However, only a few limited studies about the genetic diversity of these species were performed. In the present paper, and for the first time at such extend, we genotyped 279 O. glaberrima, selected both for their impact in current breeding and for their geographical distribution, and 101 O. barthii, chosen based on their geographic origin, using a set of 235 SNPs specifically designed for African rice diversity. Using those data, we were able to structure the individuals from our sample in three populations for O. barthii, related to geography, and two populations in O. glaberrima; these two last populations cannot be linked however to any currently phenotyped trait. Moreover, we were also able to identify misclassification in O. glaberrima as well as in O. barthii and identified new form of O. sativa from the set of African varieties.     

Climate-driven diversification in two widespread Galerida larks

Background

The major impact of Plio-Pleistocene climatic oscillations on the current genetic structure of many species is widely recognised but their importance in driving speciation remains a matter of controversies. In addition, since most studies focused on Europe and North America, the influence of many other biogeographic barriers such as the Sahara remains poorly understood. In this paper, climate-driven diversification was investigated by using a comparative phylogeographic approach in combination with phenotypic data in two avian species groups distributed on both sides of the deserts belt of Africa and Asia. In particular, we tested whether: 1) vicariance diversification events are concomitant with past climatic events; and 2) current ecological factors (using climate and competition as proxies) contribute to phenotypic divergence between allopatric populations.

Results

Mitochondrial and nuclear sequence data indicated that the crested and Thekla lark species groups diverged in the early Pliocene and that subsequent speciation events were congruent with major late Pliocene and Pleistocene climatic events. In particular, steep increase in aridity in Africa near 2.8 and 1.7 million years ago were coincident with two north-south vicariance speciation events mediated by the Sahara. Subsequent glacial cycles of the last million years seem to have shaped patterns of genetic variation within the two widespread species (G. cristata and G. theklae). The Sahara appears to have allowed dispersal from the tropical areas during climatic optima but to have isolated populations north and south of it during more arid phases. Phenotypic variation did not correlate with the history of populations, but was strongly influenced by current ecological conditions. In particular, our results suggested that (i) desert-adapted plumage evolved at least three times and (ii) variation in body size was mainly driven by interspecific competition, but the response to competition was stronger in more arid areas.

Conclusion

Climatic fluctuations of the Plio-Pleistocene strongly impacted diversification patterns in the Galerida larks. Firstly, we found that cladogenesis coincides with major climatic changes, and the Sahara appears to have played a key role in driving speciation events. Secondly, we found that morphology and plumage were strongly determined by ecological factors (interspecific competition, climate) following vicariance.     

Spatio-temporal history of the disjunct family Tecophilaeaceae: a tale involving the colonization of three Mediterranean-type ecosystems

Background and Aims

Tecophilaeaceae (27 species distributed in eight genera) have a disjunct distribution in California, Chile and southern and tropical mainland Africa. Moreover, although the family mainly occurs in arid ecosystems, it has colonized three Mediterranean-type ecosystems. In this study, the spatio-temporal history of the family is examined using DNA sequence data from six plastid regions.

Methods

Modern methods in divergence time estimation (BEAST), diversification (LTT and GeoSSE) and biogeography (LAGRANGE) are applied to infer the evolutionary history of Tecophilaeaceae. To take into account dating and phylogenetic uncertainty, the biogeographical inferences were run over a set of dated Bayesian trees and the analyses were constrained according to palaeogeographical evidence.

Key Results

The analyses showed that the current distribution and diversification of the family were influenced primarily by the break up of Gondwana, separating the family into two main clades, and the establishment of a Mediterranean climate in Chile, coinciding with the radiation of Conanthera. Finally, unlike many other groups, no shifts in diversification rates were observed associated with the dispersals in the Cape region of South Africa.

Conclusions

Although modest in size, Tecophilaeaceae have a complex spatio-temporal history. The family is now most diverse in arid ecosystems in southern Africa, but is expected to have originated in sub-tropical Africa. It has subsequently colonized Mediterranean-type ecosystems in both the Northern and Southern Hemispheres, but well before the onset of the Mediterranean climate in these regions. Only one lineage, genus Conanthera, has apparently diversified to any extent under the impetus of a Mediterranean climate.     

Human remains from the Pleistocene-Holocene transition of southwest China suggest a complex evolutionary history for East Asians

Background

Later Pleistocene human evolution in East Asia remains poorly understood owing to a scarcity of well described, reliably classified and accurately dated fossils. Southwest China has been identified from genetic research as a hotspot of human diversity, containing ancient mtDNA and Y-DNA lineages, and has yielded a number of human remains thought to derive from Pleistocene deposits. We have prepared, reconstructed, described and dated a new partial skull from a consolidated sediment block collected in 1979 from the site of Longlin Cave (Guangxi Province). We also undertook new excavations at Maludong (Yunnan Province) to clarify the stratigraphy and dating of a large sample of mostly undescribed human remains from the site.

Methodology/Principal Findings

We undertook a detailed comparison of cranial, including a virtual endocast for the Maludong calotte, mandibular and dental remains from these two localities. Both samples probably derive from the same population, exhibiting an unusual mixture of modern human traits, characters probably plesiomorphic for later Homo, and some unusual features. We dated charcoal with AMS radiocarbon dating and speleothem with the Uranium-series technique and the results show both samples to be from the Pleistocene-Holocene transition: ∼14.3-11.5 ka.

Conclusions/Significance

Our analysis suggests two plausible explanations for the morphology sampled at Longlin Cave and Maludong. First, it may represent a late-surviving archaic population, perhaps paralleling the situation seen in North Africa as indicated by remains from Dar-es-Soltane and Temara, and maybe also in southern China at Zhirendong. Alternatively, East Asia may have been colonised during multiple waves during the Pleistocene, with the Longlin-Maludong morphology possibly reflecting deep population substructure in Africa prior to modern humans dispersing into Eurasia.     

Genetic structure and diversity of coffee (Coffea) across Africa and the Indian Ocean islands revealed using microsatellites

Background and Aims

The coffee genus (Coffea) comprises 124 species, and is indigenous to the Old World Tropics. Due to its immense economic importance, Coffea has been the focus of numerous genetic diversity studies, but despite this effort it remains insufficiently studied. In this study the genetic diversity and genetic structure of Coffea across Africa and the Indian Ocean islands is investigated.

Methods

Genetic data were produced using 13 polymorphic nuclear microsatellite markers (simple sequence repeats, SSRs), including seven expressed sequence tag-SSRs, and the data were analysed using model- and non-model-based methods. The study includes a total of 728 individuals from 60 species.

Key Results

Across Africa and the Indian Ocean islands Coffea comprises a closely related group of species with an overall pattern of genotypes running from west to east. Genetic structure was identified in accordance with pre-determined geographical regions and phylogenetic groups. There is a good relationship between morpho-taxonomic species delimitations and genetic units. Genetic diversity in African and Indian Ocean Coffea is high in terms of number of alleles detected, and Madagascar appears to represent a place of significant diversification in terms of allelic richness and species diversity.

Conclusions

Cross-species SSR transferability in African and Indian Ocean islands Coffea was very efficient. On the basis of the number of private alleles, diversification in East Africa and the Indian Ocean islands appears to be more recent than in West and West-Central Africa, although this general trend is complicated in Africa by the position of species belonging to lineages connecting the main geographical regions. The general pattern of phylogeography is not in agreement with an overall east to west (Mascarene, Madagascar, East Africa, West Africa) increase in genome size, the high proportion of shared alleles between the four regions or the high numbers of exclusive shared alleles between pairs or triplets of regions.     

The importance of Anatolian mountains as the cradle of global diversity in Arabis alpina, a key arctic-alpine species

Background and Aims

Anatolia is a biologically diverse, but phylogeographically under-explored region. It is described as either a centre of origin and long-term Pleistocene refugium, or as a centre for genetic amalgamation, fed from distinct neighbouring refugia. These contrasting hypotheses are tested through a global phylogeographic analysis of the arctic–alpine herb, Arabis alpina.

Methods

Herbarium and field collections were used to sample comprehensively the entire global range, with special focus on Anatolia and Levant. Sequence variation in the chloroplast DNA trnL-trnF region was examined in 483 accessions. A haplotype genealogy was constructed and phylogeographic methods, demographic analysis and divergence time estimations were used to identify the centres of diversity and to infer colonization history.

Key Results

Fifty-seven haplotypes were recovered, belonging to three haplogroups with non-overlapping distributions in (1) North America/Europe/northern Africa, (2) the Caucuses/Iranian Plateau/Arabian Peninsula and (3) Ethiopia–eastern Africa. All haplogroups occur within Anatolia, and all intermediate haplotypes linking the three haplogroups are endemic to central Anatolia and Levant, where haplotypic and nucleotide diversities exceeded all other regions. The local pattern of haplotype distribution strongly resembles the global pattern, and the haplotypes began to diverge approx. 2·7 Mya, coinciding with the climate cooling of the early Middle Pleistocene.

Conclusions

The phylogeographic structure of Arabis alpina is consistent with Anatolia being the cradle of origin for global genetic diversification. The highly structured landscape in combination with the Pleistocene climate fluctuations has created a network of mountain refugia and the accumulation of spatially arranged genotypes. This local Pleistocene population history has subsequently left a genetic imprint at the global scale, through four range expansions from the Anatolian diversity centre into Europe, the Near East, Arabia and Africa. Hence this study also illustrates the importance of sampling and scaling effects when translating global from local diversity patterns during phylogeographic analyses.