Further support for a Palaearctic origin of Leishmania

The fossil record and systematics of murid rodents, reservoirs of zoonotic cutaneous leishmaniasis in the Palaearctic, Oriental, African, Nearctic and Neotropical, strongly support a Palaearctic origin of Leishmania. The fossil record and systematics of phlebotomine sand flies reinforce this idea. Interpretations of molecular data that place the origin of Leishmania in the Neotropical are inconsistent with the natural histories of reservoirs and vectors. The evolutionary pattern of New World rats (Sigmodontinae) indicates that they may be the most important reservoirs of zoonotic cutaneous leishmaniasis throughout their range.     

Phylodynamics of HIV-1 Subtype C Epidemic in East Africa

The HIV-1 subtype C accounts for an important fraction of HIV infections in east Africa, but little is known about the genetic characteristics and evolutionary history of this epidemic. Here we reconstruct the origin and spatiotemporal dynamics of the major HIV-1 subtype C clades circulating in east Africa. A large number (n = 1,981) of subtype C pol sequences were retrieved from public databases to explore relationships between strains from the east, southern and central African regions. Maximum-likelihood phylogenetic analysis of those sequences revealed that most (>70%) strains from east Africa segregated in a single regional-specific monophyletic group, here called C_EA. A second major Ethiopian subtype C lineage and a large collection of minor Kenyan and Tanzanian subtype C clades of southern African origin were also detected. A Bayesian coalescent-based method was then used to reconstruct evolutionary parameters and migration pathways of the C_EA African lineage. This analysis indicates that the C_EA clade most probably originated in Burundi around the early 1960s, and later spread to Ethiopia, Kenya, Tanzania and Uganda, giving rise to major country-specific monophyletic sub-clusters between the early 1970s and early 1980s. The results presented here demonstrate that a substantial proportion of subtype C infections in east Africa resulted from dissemination of a single HIV local variant, probably originated in Burundi during the 1960s. Burundi was the most important hub of dissemination of that subtype C clade in east Africa, fueling the origin of new local epidemics in Ethiopia, Kenya, Tanzania and Uganda. Subtype C lineages of southern African origin have also been introduced in east Africa, but seem to have had a much more restricted spread.     

High-level phylogeny of early Tertiary rodents: dental evidence

Major crown‐groups of rodents were well established in the early Tertiary, and fossils provide an invaluable window into their evolutionary history. The main focus of this project was to perform a cladistic assessment of the dental evidence for early Tertiary rodent cladogenesis – the masticatory apparatus and teeth are the most frequently preserved anatomical features in the fossil record. We focused on groups that existed in a period corresponding to their early history, combining fossils belonging to extinct lineages and to stem‐groups leading to modern lineages. While the monophyly of some groups is not systematically explored, our results have important implications for high‐level rodent relationships and systematics. These results are consistent with those of recent molecular phylogenies and reliably congruent with the stratigraphic record, thus enhancing the pertinence of dental characters for phylogenetic inference. Our approach provides evidence of a fundamental dichotomy in early rodent history. Two major clades have been identified: (1) the earliest ‘ctenodactyloid’ (Ctenodactylidae, Chapattimyidae, Yuomyidae, Diatomyidae) and hystricognathous (Tsaganomyidae, Baluchimyinae, ‘phiomorphs’, ‘caviomorphs’) rodents, and (2) the earliest ‘ischyromyoid’ rodents with their closest relatives (Muroidea + Dipodoidea + Geomyoidea + Anomaluroidea + Castoroidea + Sciuravidae + Gliroidea, and Sciuroidea + Aplodontoidea + Theridomorpha). This topology has led us to endorse Ctenohystrica as the first clade and propose a new taxon, Ischyromyiformes, for the second. Although minimized in our working hypothesis, the homoplasy in dental characters remains significant. However, a number of homoplasic characters reveal structuring in their internal distribution, allowing us to discern evolutionary morphological patterns, notably the pentalophodonty of molars, zygomasseteric complex and incisor enamel microstructure. © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society, 2004, 142 , 105–134.     

Vegetational patterns and distribution of relict taxa in humid temperate forests and wetlands of Georgia (Transcaucasia)

Small-scale vegetational patterns of Georgian lowland and montane forests and wetlands are documented by species per vegetation unit, function of species in particular vegetation units and vegetational sketches. The humid warm-temperate climate of western Georgia contributes to a different spatial pattern than known for most of Europe. One characteristic feature of western Georgian relict vegetation is the co-occurrence of 'Mediterranean', 'Sub-mediterranean', temperate, and Tertiary relict species, as well as of species normally confined to either zonal or azonal vegetation, in the same or closely related vegetation units. The extant distribution of Tertiary relict taxa strongly depends on how they are niching into changing environments. Niching strategies are assumed crucial for extinction or survival in times of rapid climatic/environmental changes. For Tertiary relict plant taxa in western Georgia we found four different niching strategies which also hold true of other northern hemispheric Tertiary relict plant taxa. Some amphibians and reptiles display similar distribution patterns and niching strategies as do relict plant taxa. A number of relict taxa in the warm humid regions of western Georgia occupy niches in swamp forests which might represent 'primeval' environments of species which are at present also elements of meso-Mediterranean vegetation and of thermophilous forest edges and hedges in Central Europe.     

African DNA Lineages in the Mitochondrial Gene Pool of Europeans

Mitochondrial DNA (mtDNA) nucleotide sequences of African origin are found in various European populations at a low frequency (on average, less than 1%). Data on mtDNA variation in Eurasian and African populations have been analyzed, and African mtDNA lineages have been found in Europeans. It has been demonstrated that, despite the high diversity of mtDNA haplotypes of African origin in Europeans, few monophyletic clusters of African lineages are characterized by long-term diversity formed in Europe. Only two such mtDNA clusters (from haplogroups L1b and L3b) have been found, their evolutionary age not exceeding 6500 years. European and African populations have been compared with respect to the frequency distributions of the alleles of autosomal microsatellite loci found in Russian carriers of African mtDNA haplotypes. It has been demonstrated that alleles typical of Europeans are characteristic of the autosomal genotypes of these Russian individuals.     

Genetic data from the extinct giant rat from Tenerife (Canary Islands) points to a recent divergence from mainland relatives

Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, according to which gigantism arises in originally small-sized species and dwarfism in large ones. Species of extinct insular giant rodents are known from all over the world. In the Canary Islands, two examples of giant rats, †Canariomys bravoi and †Canariomys tamarani, endemic to Tenerife and Gran Canaria, respectively, disappeared soon after human settlement. The highly derived morphological features of these insular endemic rodents hamper the reconstruction of their evolutionary histories. We have retrieved partial nuclear and mitochondrial data from †C. bravoi and used this information to explore its evolutionary affinities. The resulting dated phylogeny confidently places †C. bravoi within the African grass rat clade (Arvicanthis niloticus). The estimated divergence time, 650 000 years ago (95% higher posterior densities: 373 000–944 000), points toward an island colonization during the Günz–Mindel interglacial stage. †Canariomys bravoi ancestors would have reached the island via passive rafting and then underwent a yearly increase of mean body mass calculated between 0.0015 g and 0.0023 g; this corresponds to fast evolutionary rates (in darwins (d), ranging from 7.09 d to 2.78 d) that are well above those observed for non-insular mammals.     

Evolutionary genomics of chromoviruses in eukaryotes

The diversity, origin, and evolution of chromoviruses in Eukaryota were examined using the massive amount of genome sequence data for different eukaryotic lineages. A surprisingly large number of novel full-length chromoviral elements were found, greatly exceeding the number of the known chromoviruses. These new elements are mostly structurally intact and highly conserved. Chromoviruses in the key Amniota lineage, the reptiles, have been analyzed by PCR to explain their evolutionary dynamics in amniotes. Phylogenetic analyses provide evidence for a novel centromere-specific chromoviral clade that is widespread and highly conserved in all seed plants. Chromoviral diversity in plants, fungi, and vertebrates, as shown by phylogenetic analyses, was found to be much greater than previously expected. The age of plant chromoviruses has been significantly extended by finding their representatives in the most basal plant lineages, the green and the red algae. The evolutionary origin of chromoviruses has been found to be no earlier than in Cercozoa. The evolutionary history and dynamics of chromoviruses can be explained simply by strict vertical transmission in plants, followed by more complex evolution in fungi and in Metazoa. The currently available data clearly show that chromoviruses indeed represent the oldest and the most widespread clade of Metaviridae.     

Linking the molecular evolution of avian beta (β) keratins to the evolution of feathers

Feathers of today's birds are constructed of beta (β)-keratins, structural proteins of the epidermis that are found solely in reptiles and birds. Discoveries of "feathered dinosaurs" continue to stimulate interest in the evolutionary origin of feathers, but few studies have attempted to link the molecular evolution of their major structural proteins (β-keratins) to the appearance of feathers in the fossil record. Using molecular dating methods, we show that before the appearance of Anchiornis (～155 Million years ago (Ma)) the basal β-keratins of birds began diverging from their archosaurian ancestor ～216?Ma. However, the subfamily of feather β-keratins, as found in living birds, did not begin diverging until ～143?Ma. Thus, the pennaceous feathers on Anchiornis, while being constructed of avian β-keratins, most likely did not contain the feather β-keratins found in the feathers of modern birds. Our results demonstrate that the evolutionary origin of feathers does not coincide with the molecular evolution of the feather β-keratins found in modern birds. More likely, during the Late Jurassic, the epidermal structures that appeared on organisms in the lineage leading to birds, including early forms of feathers, were constructed of avian β-keratins other than those found in the feathers of modern birds. Recent biophysical studies of the β-keratins in feathers support the view that the appearance of the subfamily of feather β-keratins altered the biophysical nature of the feather establishing its role in powered flight.     

Dimetrodon Is Not a Dinosaur: Using Tree Thinking to Understand the Ancient Relatives of Mammals and their Evolution

The line of descent that includes all living mammals extends back in time over 300 million years. Many of the ancient relatives of mammals that fall along this line are very different in appearance from living mammals and are frequently mistaken for reptiles such as dinosaurs. This misconception is reinforced by the fact that these animals are often referred to as “mammal-like reptiles,” a term reflecting outdated methods for classifying organisms. In reality, these ancient mammal-relatives, known as synapsids, are more closely related to living mammals than they are to any reptiles. Evolutionary trees, which depict patterns of descent from common ancestors among organisms, are very useful for understanding why this is the case and for reconstructing the evolutionary histories of many of the unique characters found in mammals. Here, I provide an introduction to evolutionary trees and their implications for understanding the relationships between mammals, synapsids, and reptiles. This is followed by a review of synapsid diversity and a discussion of how evolutionary trees can be used to investigate when in synapsid history different mammalian characteristics first appeared.     

Molecular evidence for a clade of turtles.

Although turtles have been generally grouped with the most primitive reptile species, the origin and phylogenetic relationships of turtles have remained unresolved to date. To confirm the phylogenetic position of turtles in amniotes, we have cloned and determined the cDNA sequences encoding for skink lactate dehydrogenase (LDH)-A and LDH-B, snake LDH-A, and African clawed frog LDH-A; four alpha-enolase cDNA sequences from turtle, alligator, skink, and snake were also cloned and determined. All of these eight cDNA sequences, as well as the previously published LDH-A, LDH-B, and alpha-enolase of mammals, birds, reptiles, and African clawed frog, were analyzed by the phylogenetic tree reconstruction methods of neighbor-joining, maximum parsimony, and maximum likelihood. In the phylogenetic analyses, the turtle was found to be closely related to the alligator. Also, we found that the turtle had diverged after the divergence of squamates and birds. This departs from previous hypotheses of turtle evolution and further suggests that turtles are the latest of divergent reptiles, having been derived from an ancestor of crocodilian lineage within the last 200 million years.     

Genome size, GC percentage and 5mC level in the Indonesian coelacanth Latimeria menadoensis

The living fossil Latimeria menadoensis is important to understand sarcopterygian evolution. To gain further insights into this fish species we studied its genome size, GC% and 5mC level. The genome size and the GC% of the Indonesian coelacanth seem to be very similar to those of the African coelacanth. Moreover the GC%, the CpG frequency and the 5mC level of L. menadoensis are more similar to those of fish and amphibians than to those of mammals, birds and reptiles and this is in line with the hypothesis that two different DNA methylation and CpG shortage equilibria arose during vertebrate evolution. Our results suggest that the genome of L. menadoensis has remained unchanged for several million years, maybe since the origin of the lineage which from lobe-finned fish led to tetrapods. These data fit a conservative evolutionary landscape and suggest that the genome of the extant crossopterygians may be a sort of evolutionarily frozen genome.     

The interrelationships between the African and South American Rodents and their bearing on the problem of the origin of South American monkeys

The first presence of Primates in South American Oligocene, at the same time as the Rodents, suggests a similar history. The anatomical similarities between African (Phiomorpha) and South American (Caviomorpha) rodents cannot satisfactorily be explained without direct relationships. As a consequence of continental drift, the migration by rafts, if not easy, was certainly possible in early Tertiary. The same is true for Primates.     

The Chikungunya threat: an ecological and evolutionary perspective

Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus. Although primarily African and zoonotic, it is known chiefly for its non-African large urban outbreaks during which it is transmitted by the same vectors as those of Dengue viruses. Unlike Dengue viruses, CHIKV displays a re-emergence pattern that closely depends on long-distance migrations including recent re-immigrations from African (putatively zoonotic) sources. Genus-based differences also emerged when comparing the evolution of Dengue-related (Flaviviruses) and of CHIKV-related (Alphaviruses) arboviruses. In this review, we discuss current information on CHIKV genetics, ecology and human infection. Further investigations on African CHIKV ecology and the differences between Flavivirus and Alphavirus members in adaptive changes and evolutionary constraints are likely to help delineate the potential of further CHIKV (re-)emergence.     

Analysis of introduction history of invasive plants in Brazil reveals patterns of association between biogeographical origin and reason for introduction

Knowledge of historical factors associated with biological invasions in a region can help identify source regions, vectors and pathways more likely to originate potential invaders as well as prioritize resource allocation for selective prevention and early detection strategies. In Brazil, little is known about the introduction history of many invasive plant species, and analyses of historical factors associated with invasions are lacking. To fill this gap, I used a dataset of 117 invasive alien plants across 13 habitats in Brazil to identify potential patterns of continent of origin, reason for introduction, and to test the hypotheses that (i) more Eurasian species are invasive in Brazil than species native from other continents, that (ii) more horticultural species are invasive in Brazil than species introduced for other reasons, and that (iii) continent of origin and reason for introduction are associated. I found that significantly more invasive plant species in Brazil are native to Africa and Asia, were introduced for horticulture and forage, and are part of the families Poaceae, Fabaceae, and Pinaceae. I also found a significant association between continent of origin and reason for introduction, with more invasive species than average being African forage grasses and Asian agroforestry or ornamental plants. In conclusion, the results suggest that the current invasive alien flora of Brazil results from the combination of patterns of recent human migration waves and deliberate species introductions for technological and commercial reasons. These results can help prioritize invasive species and vectors in prevention, early detection, and control strategies.     

The evolution of HIV-1 and the origin of AIDS

The major cause of acquired immune deficiency syndrome (AIDS) is human immunodeficiency virus type 1 (HIV-1). We have been using evolutionary comparisons to trace (i) the origin(s) of HIV-1 and (ii) the origin(s) of AIDS. The closest relatives of HIV-1 are simian immunodeficiency viruses (SIVs) infecting wild-living chimpanzees (Pan troglodytes troglodytes) and gorillas (Gorilla gorilla gorilla) in west central Africa. Phylogenetic analyses have revealed the origins of HIV-1: chimpanzees were the original hosts of this clade of viruses; four lineages of HIV-1 have arisen by independent cross-species transmissions to humans and one or two of those transmissions may have been via gorillas. However, SIVs are primarily monkey viruses: more than 40 species of African monkeys are infected with their own, species-specific, SIV and in at least some host species, the infection seems non-pathogenic. Chimpanzees acquired from monkeys two distinct forms of SIVs that recombined to produce a virus with a unique genome structure. We have found that SIV infection causes CD4⁺ T-cell depletion and increases mortality in wild chimpanzees, and so the origin of AIDS is more ancient than the origin of HIV-1. Tracing the genetic changes that occurred as monkey viruses adapted to infect first chimpanzees and then humans may provide insights into the causes of the pathogenicity of these viruses.     

Asynchronous colonization of Madagascar by the four endemic clades of primates, tenrecs, carnivores, and rodents as inferred from nuclear genes

Madagascar harbors four large adaptive radiations of endemic terrestrial mammals: lemurs, tenrecs, carnivorans, and rodents. These rank among the most spectacular examples of evolutionary diversification, but their monophyly and origins are debated. The lack of Tertiary fossils from Madagascar leaves molecular studies as most promising to solve these controversies. We provide a simultaneous reconstruction of phylogeny and age of the four radiations based on a 3.5-kb data set from three nuclear genes (ADRA2B, vWF, and AR). The analysis supports each as a monophyletic clade, sister to African taxa, and thereby identifies four events of colonization out of Africa. To infer the time windows for colonization, we take into account both the divergence from the closest non-insular sister group and the initial intra-insular radiation, which is a novel but conservative approach in studies of the colonization history of Madagascar. We estimate that lemurs colonized Madagascar between 60 million years ago (Mya) (split from lorises) and 50 Mya (lemur radiation) (70-41 Mya taking 95% credibility intervals into account), tenrecs between 42 and 25 Mya (50-20 Mya), carnivorans between 26 and 19 Mya (33-14 Mya), and rodents between 24 and 20 Mya (30-15 Mya). These datings suggest at least two asynchronous colonization events: by lemurs in the Late Cretaceous-Middle Eocene, and by carnivorans and rodents in the Early Oligocene-Early Miocene. The colonization by tenrecs may have taken place simultaneously with either of these two events, or in a third event in the Late Eocene-Oligocene. Colonization by at least lemurs, rodents, and carnivorans appears to have occurred by overseas rafting rather than via a land bridge hypothesized to have existed between 45 and 26 Mya, but the second scenario cannot be ruled out if credibility intervals are taken into account.     

REPTILIAN VIVIPARITY AND DOLLO'S LAW

It has been suggested repeatedly that the evolutionary transition from oviparity (egg-laying) to viviparity (live-bearing) in reptiles is irreversible. However, these adaptive arguments have yet to be tested by detailed examination of the phylogenetic distribution of oviparity and viviparity across a broad range of taxa. Using available data on reproductive modes and phylogenetic relationships within reptiles, we here quantify the numbers and directions of evolutionary transitions between oviparity and viviparity. Phylogenetic relationships among three diverse squamate groups (scincid lizards, colubrid snakes, elapid snakes) are currently inadequately known for inclusion in this study Among the remaining reptiles, oviparity has given rise to viviparity at least 35 times. Five possible instances of reversals (from viviparity to oviparity) are identified, but closer examination indicates that all have weak empirical support (i.e., they could be “unreversed” with little loss in parsimony, and/or are based on poorly substantiated phylogenetic hypotheses). Viviparity is clearly more frequently (and presumably easily) gained than lost in several disparate groups so far examined (reptiles, fishes, polychaete worms); this evolutionary bias should be considered when reproductive mode is optimized on a phylogeny or employed in phylogenetic reconstruction.     

Phylogenetic and molecular evolution of the ADAM (A Disintegrin And Metalloprotease) gene family from Xenopus tropicalis, to Mus musculus, Rattus norvegicus, and Homo sapiens

ADAM (a disintegrin and metalloprotease) genes have been identified in various tissues and species, and recently associated with several important human diseases such as tumor and asthma. Although various biological processes have been known for the ADAM family in different species including fertilization, neurogenesis, infection and inflammation, little is known about its detailed phylogenetic and molecular evolutionary history. In this study, the ADAMs of Xenopus (Silurana) tropicalis, Mus musculus, Rattus norvegicus, and Homo sapiens were collected and analyzed by using the Bayesian analysis and gene synteny analysis to establish a comprehensive phylogenetic relationship and evolutionary drive of this gene family. It was found that there were more ADAMs in the two rodents than in the amphibian, suggesting an expansion of the ADAM gene family during the early evolution of mammals. All ADAMs from this expansion were retained in both the rodents, but other duplication events occurred subsequently in the two rodents, respectively, leading to the classification of rodent ADAMs as classes I, II and III. Moreover, these duplicated ADAM genes in the rodents were found to be driven by positive selection, which might be the major force to retain them in the genome. Importantly, it was also found that orthologs of ADAM3 and 5 have been lost in humans. These results not only provide valuable information of the evolution of ADAM genes, but may also help in understanding the role of ADAM genes in the pathobiology of relevant diseases.     

An overview of endosymbiotic models for the origins of eukaryotes, their ATP-producing organelles (mitochondria and hydrogenosomes), and their heterotrophic lifestyle.

The evolutionary processes underlying the differentness of prokaryotic and eukaryotic cells and the origin of the latter's organelles are still poorly understood. For about 100 years, the principle of endosymbiosis has figured into thoughts as to how these processes might have occurred. A number of models that have been discussed in the literature and that are designed to explain this difference are summarized. The evolutionary histories of the enzymes of anaerobic energy metabolism (oxygen-independent ATP synthesis) in the three basic types of heterotrophic eukaryotes those that lack organelles of ATP synthesis, those that possess mitochondria and those that possess hydrogenosomes--play an important role in this issue. Traditional endosymbiotic models generally do not address the origin of the heterotrophic lifestyle and anaerobic energy metabolism in eukaryotes. Rather they take it as a given, a direct inheritance from the host that acquired mitochondria. Traditional models are contrasted to an alternative endosymbiotic model (the hydrogen hypothesis), which addresses the origin of heterotrophy and the origin of compartmentalized energy metabolism in eukaryotes.     

New evidence of hexaploidy in' large' African Barbus with some considerations on the origin of hexaploidy

Three species of' large' African Barbus from the Republic of Guinea (West Africa), were characterized by the chromosome numbers (2N) of 148 (B. bynni occidentalis and B. wurtzi ) and 150 (B. petitjeani Daget, 1962). All these species have a karyotype which corresponds to the evolutionary hexaploid level. The karyotype of B. petitjeani is composed of chromosomes clearly grouped into morphologically homomorphic sextets which may document the origin of hexaploidy via an autopolyploidic event. Present findings extend the known distribution of evolutionary hexaploidy in' large' African Barbus to West Africa and show evidence of the pan-African distribution of this phenomenon.