Evidence of a cenozoic Betic-Kabilian connection based on freshwater fish phylogeography (Luciobarbus, Cyprinidae)

The phylogenetic relationships among 26 species of the subgenus Luciobarbus were examined through comparison of the complete sequence of the mitochondrial genes ATPase 6 and 8 and cytochrome b. The monophyletic condition of the Luciobarbus subgenus was confirmed by several data treatment methods. Findings indicate a closer relationship among species inhabiting Caucasian, Greek, and North African areas than between the latter and those of the Iberian region. The isolation of these main clades is postulated to have occurred after the Messinian salinity crisis (5.5 MY ago) when the Iberian Peninsula broke away from the African continent. Based on a calibrated molecular clock proposed herein, the subsequent splitting of this subgenus corresponds to the isolation of the other three areas (Caucasian, Greek, and North African) about 4.5 MY ago, which would have interrupted any possible gene flow between lineages. However, the present data indicate that the North African Kabilies Mountain area maintained its contact with the south Iberian Peninsula for a longer period.     

Phylogenetic relationships and divergence time estimate of African anguilliform catfish (Siluriformes: Clariidae) inferred from ribosomal gene and spacer sequences

The catfish family Clariidae comprises species in which the body shape ranges from fusiform to anguilliform. Recent studies have shown that this body elongation is the result of convergent evolution. This paper aims to study the evolution towards anguilliformity in a phylogenetic framework. Sequences of 29 taxa were analyzed using the neighbor-joining, maximum-likelihood, maximum-parsimony, and Bayesian inference algorithms and the parsimony algorithm in POY. The study yields phylogenetic hypotheses showing well-supported clades. Anguilliformity appears to have arisen at least four times, each time having a sister group relation with a fusiform Clarias-like ancestor. Divergence time estimation indicates that the African Clariidae started radiating between 123 and 56 My ago.     

The Wilhelmine E. Key 2001 Invitational Lecture. Estimation of divergence times for a few mammalian and several primate species

Statistical methods for estimating divergence times by using multiprotein gamma distances are discussed. When a large number of proteins are used, even a small degree of deviation from the molecular clock hypothesis can be detected. In this case, one may use the stem-lineage method for estimating divergence times. However, the estimates obtained by this method are often similar to those obtained by the linearized tree method. Application of these methods to a dataset of 104 proteins from several vertebrate species indicated that the divergence times between humans and mice and between mice and rats are about 96 and 33 million years (MY) ago, respectively. These estimates were obtained by assuming that birds and mammals diverged 310 MY ago. Similarly application of the methods to the protein sequence data from primate species indicated that the human lineage separated from the chimpanzee, gorilla, Old World monkeys, and New World monkeys about 6.0, 7.0, 23.0, and 33.0 MY ago, respectively. In this case the use of two calibration points, that is, the divergence time (13 MY ago) between humans and orangutans and between primates and artiodactyls (90 MY ago) gave essentially the same estimates.     

Multigene Phylogenetics Reveals Temporal Diversification of Major African Malaria Vectors

The major vectors of malaria in sub-Saharan Africa belong to subgenus Cellia. Yet, phylogenetic relationships and temporal diversification among African mosquito species have not been unambiguously determined. Knowledge about vector evolutionary history is crucial for correct interpretation of genetic changes identified through comparative genomics analyses. In this study, we estimated a molecular phylogeny using 49 gene sequences for the African malaria vectors An. gambiae, An. funestus, An. nili, the Asian malaria mosquito An. stephensi, and the outgroup species Culex quinquefasciatus and Aedes aegypti. To infer the phylogeny, we identified orthologous sequences uniformly distributed approximately every 5 Mb in the five chromosomal arms. The sequences were aligned and the phylogenetic trees were inferred using maximum likelihood and neighbor-joining methods. Bayesian molecular dating using a relaxed log normal model was used to infer divergence times. Trees from individual genes agreed with each other, placing An. nili as a basal clade that diversified from the studied malaria mosquito species 47.6 million years ago (mya). Other African malaria vectors originated more recently, and independently acquired traits related to vectorial capacity. The lineage leading to An. gambiae diverged 30.4 mya, while the African vector An. funestus and the Asian vector An. stephensi were the most closely related sister taxa that split 20.8 mya. These results were supported by consistently high bootstrap values in concatenated phylogenetic trees generated individually for each chromosomal arm. Genome-wide multigene phylogenetic analysis is a useful approach for discerning historic relationships among malaria vectors, providing a framework for the correct interpretation of genomic changes across species, and comprehending the evolutionary origins of this ubiquitous and deadly insect-borne disease.     

A three-genome phylogeny of Momordica (Cucurbitaceae) suggests seven returns from dioecy to monoecy and recent long-distance dispersal to Asia

The bitter gourd genus Momordica comprises 47 species in Africa and 12 in Asia and Australia. All have unisexual flowers, and of the African species, 24 are dioecious, 23 monoecious, while all Asian species are dioecious. Maximum likelihood analyses of 6257 aligned nucleotides of plastid, mitochondrial and nuclear DNA obtained for 122 accessions of Momordica and seven outgroups show that Momordica is monophyletic and consists of 11 well-supported clades. Monoecy evolved from dioecy seven times independently, always in Africa and mostly in savanna species with low population densities. Leaky dioecy, with occasional fruit-producing males, occurs in two African species and might be the first step in an evolutionary transition towards monoecy. Dated biogeographic analyses suggest that Momordica originated in tropical Africa and that the Asian species are the result of one long-distance dispersal event about 19 million years ago. The pantropical vegetable Momordica charantia is of African, not Asian origin as had previously been suggested.     

MOLECULAR GENETIC-DISTANCE ESTIMATES AMONG THE URSIDAE AS INDICATED BY ONE- AND TWO-DIMENSIONAL PROTEIN ELECTROPHORESIS

Evolutionary relationships among eight species of Ursidae (including the giant panda) relative to two Procyonidae species (raccoon and red panda) were estimated based on the extent of electrophoretic variation of 289 radiolabelled fibroblast proteins resolved by two-dimensional gel electrophoresis and among 44 isozyme loci resolved by one-dimensional electrophoresis. Allelic differences among these species were converted to genetic distances, and phenetic trees were constructed. In addition, the electrophoretic data were coded as unit characters, and minimum-length trees were derived based on the Wagner method using maximum parsimony. Regardless of the tree-building method employed, the data sets agreed on the following branching sequence: between 22.4 and 32.3 million years (MY) ago, the ancestors of the procyonids and the ursids split into two lineages. Within 10 MY, the red panda split from the line that led to the raccoon. An ancestor of the giant panda split from the ursid line 18–22 MY ago, and the South American spectacled bear split from the line leading to ursine bears 10.5–15.0 MY B.P. A group of six closely related ursine bears (brown bear, polar bear, Asiatic black bear, Malayan sun bear, American black bear, and sloth bear) diverged from a common ancestor during the past 4–8 MY. Much of this ursine radiation was not resolved by our results, with the exception of a recent (2–3 MY B.P.) divergence of brown bear and polar bear. The topological concordance of the data sets from one- and two-dimensional electrophoresis supports the usefulness of these procedures for evolutionary inference and provides additional precision to the reconstruction of divergence nodes of this carnivore group.     

Land, lake, and fish: Investigation of fish remains from Gesher Benot Ya'aqov (paleo-Lake Hula)

The question of whether or not pre-modern hominins were responsible for the accumulation of fish remains is discussed through analyses of remains recovered from two lacustrine facies (I-4 and I-5) from Area A of the Acheulian site of Gesher Benot Ya‘aqov (GBY) in the Jordan Rift Valley, Israel. The fish remains provide the first glimpse into the naturally accumulated fish assemblage from the fluctuating shores of a lake that had been continually exploited by early hominins some 780,000 years ago. Preliminary analysis of the remains show that thirteen of the seventeen species native to Lake Hula were identified at GBY. These represent three of the five freshwater fish families native to the lake: Cyprinidae (carps), Cichlidae (tilapini, St. Peter's fish), and Clariidae (catfish). From a taphonomical perspective, a significant difference is found between the two lithofacies (Layers I-4 and I-5) in terms of species composition, richness, diversity, and skeleton completeness. It appears that the fish remains recovered from Layer I-4 (clay) are better preserved than those from Layer I-5 (coquina). In both lithofacies, Cyprinidae are highly abundant while Cichlidae and Clariidae are rare and under-represented, especially when compared to the Lake Hula fishery report from the 1950s. All of these identified species may have contributed significantly to the diet of GBY hominins.     

Molecular phylogenetic analyses of snakeheads (Perciformes: Channidae) using mitochondrial DNA sequences

Mitochondrial DNA sequences of approximately 1.5 kbp including the NADH dehydrogenase subunit 2 (ND2) gene and its flanking gene regions were determined for 20 species from the freshwater fish family Channidae and 3 species from Nandidae, Badidae, and Osphronemidae. Channa orientalis and C. gachua had an approximately 170-bp insertion between the tRNA^Met and ND2 genes, where a 5′-half of the insertion was similar to the 5′-end portion of the ND2 gene and a 3′-half was homologous to the tRNA^Met gene. This insertion may thus have originated from a tandem gene duplication that occurred in a common ancestor of these two sister species. Molecular phylogenetic analyses from different tree-building methods consistently suggested the mutual monophyly of the African and Asian taxa and the existence of several clades within the Asian taxa, some of which correspond to distinct morphological features. Our molecular phylogeny clearly supported multiple independent losses of pelvic fins on Asian lineages in parallel. Divergence time estimation based on some reasonable assumptions without assuming the molecular clock suggested the early Cretaceous divergence of the African and Asian channids. The results thus support an ancient vicariant divergence of the African and Asian channids, rather than the more recent dispersal between African and Eurasian continents.     

Origin and evolution of Schistosoma japonicum

In his hypothesis on the coevolution of Asian schistosomes and snails, Davis implies that the ancestors of the Schistosoma japonicum and S. indicum species group were African and arrived in Asia via the Indian plate. This paper briefly reviews molecular phylogenetic relationships among species of the genus Schistosoma to test Davis’ theory about the origin and evolution of S. japonicum. All analyses using DNA base sequences, mitochondrial genome gene order and C-banding patterns suggest that Schistosoma originated in Asia and not Africa.     

Molecular and morphological evidence on the phylogeny of the Elephantidae

The African and Asian elephants and the mammoth diverged ca. 4-6 million years ago and their phylogenetic relationship has been controversial. Morphological studies have suggested a mammoth Asian elephant relationship, while molecular studies have produced conflicting results. We obtained cytochrome b sequences of up to 545 base pairs from five mammoths, 14 Asian and eight African elephants. A high degree of polymorphism is detected within species. With a dugong sequence used as the outgroup, parsimony and maximum-likelihood analyses support a mammoth African elephant clade. As the dugong is a very distant outgroup, we employ likelihood analysis to root the tree with a molecular clock, and use bootstrap and Bayesian analyses to quantify the relative support for different topologies. The analyses support the mammoth African elephant relationship, although other trees cannot be rejected. Ancestral polymorphisms may have resulted in gene trees differing from the species phylogeny Examination of morphological data, especially from primitive fossil members, indicates that some supposed synapomorphies between the mammoth and Asian elephant are variable, others convergent or autapomorphous. A mammoth African elephant relationship is not excluded. Our results highlight the need, in both morphological and molecular phylogenetics, for multiple markers and close attention to within-taxon variation and outgroup selection.     

MtDNA phylogeny and biogeography of Copelatinae, a highly diverse group of tropical diving beetles (Dytiscidae)

Copelatinae is a diverse lineage of diving beetles (Dytiscidae) frequently encountered in wet tropical and subtropical forests, but phylogenetic relationships are very poorly understood. We performed a phylogenetic and biogeographic analysis of this worldwide distributed group based on 50 species including a representative sample of major taxonomic groups and biogeographical regions. DNA sequences were obtained for the mitochondrial genes cytochrome oxidase I, cytochrome b, and 16S rRNA, for a total of 1575 aligned nucleotide positions. We found Copelatinae to be monophyletic, placed in a derived position and not sister to all remaining dytiscids, as had been suggested by earlier authors. The largest genus, Copelatus with some 460 known species was paraphyletic with respect to the smaller genera Lacconectus and Aglymbus. Among the major lineages of Copelatus, the subgenus Papuadytes was consistently recovered as sister to all other species (including Lacconectus and Aglymbus) with the possible exception of two western Palearctic taxa. We propose that the subgenus Papuadytes is removed from Copelatus and assigned generic status. Likewise, the two western Palearctic Copelatus are removed from this genus, and assigned the available genus name Liopterus. Our best phylogenetic hypothesis retrieved Afrotropical and New Guinean plus Australian species of Copelatus as monophyletic. Asian species were paraphyletic with respect to a species from Sulawesi which grouped with the species from New Guinea. Asian species were also paraphyletic with respect to Oriental Lacconectus, which was grouped with a clade of Neotropical species. Neotropical Copelatus form at least two separate lineages. The biogeographical evolution of Papuadytes is consistent with the relative age of the landmasses in the Austral region. Basal species are Australian, and successively derived ones are from New Caledonia and New Guinea. One species apparently dispersed from New Caledonia to China. Assuming a molecular clock and using a standard calibration of 2% divergence/MY the origin of Copelatinae is estimated to be between 85 and 95 MY.     

A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution

The African clawed frogs (Silurana and Xenopus), model organisms for scientific inquiry, are unusual in that allopolyploidization has occurred on multiple occasions, giving rise to tetraploid, octoploid, and dodecaploid species. To better understand their evolution, here we estimate a mitochondrial DNA phylogeny from all described and some undescribed species. We examine the timing and location of diversification, and test hypotheses concerning the frequency of polyploid speciation and taxonomy. Using a relaxed molecular clock, we estimate that extant clawed frog lineages originated well after the breakup of Gondwana, about 63.7 million years ago, with a 95% confidence interval from 50.4 to 81.3 million years ago. Silurana and two major lineages of Xenopus have overlapping distributions in sub-Saharan Africa, and dispersal-vicariance analysis suggests that clawed frogs originated in central and/or eastern equatorial Africa. Most or all extant species originated before the Pleistocene; recent rainforest refugia probably acted as "lifeboats" that preserved existing species, rather than "species pumps" where many new successful lineages originated. We estimate that polyploidization occurred at least six times in clawed frogs.     

Genetic evidence for the origin of Aedes aegypti,the yellow fever mosquito,in the southwestern Indian Ocean

Aedes aegypti is among the best‐studied mosquitoes due to its critical role as a vector of human pathogens and ease of laboratory rearing. Until now, this species was thought to have originated in continental Africa, and subsequently colonized much of the world following the establishment of global trade routes. However, populations of this mosquito on the islands in the southwestern Indian Ocean (SWIO), where the species occurs with its nearest relatives referred to as the Aegypti Group, have received little study. We re‐evaluated the evolutionary history of Ae. aegypti and these relatives, using three data sets: nucleotide sequence data, 18,489 SNPs and 12 microsatellites. We found that: (a) the Aegypti Group diverged 16 MYA (95% HPD: 7–28 MYA) from its nearest African/Asian ancestor; (b) SWIO populations of Ae. aegypti are basal to continental African populations; (c) after diverging 7 MYA (95% HPD: 4–15 MYA) from its nearest formally described relative (Ae. mascarensis), Ae. aegypti moved to continental Africa less than 85,000 years ago, where it recently (<1,000 years ago) split into two recognized subspecies Ae. aegypti formosus and a human commensal, Ae. aegypti aegypti; (d) the Madagascar samples form a clade more distant from all other Ae. aegypti than the named species Ae. mascarensis, implying that Madagascar may harbour a new cryptic species; and (e) there is evidence of introgression between Ae. mascarensis and Ae. aegypti on Réunion, and between the two subspecies elsewhere in the SWIO, a likely consequence of recent introductions of domestic Ae. aegypti aegypti from Asia.     

古DNA的新发现支持现代人东亚起源说

1983年,科学家们根据线粒体DNA（mtDNA）系统发育树构建了首个现代人起源的分子模型,认为现代人起源于亚洲,但1987年非洲起源说的提出取代了这一亚洲起源说。非洲起源说所依赖的无限多位点假说以及分子钟假说后来被普遍认为是错误的且不切实际的。我们近几年提出了一个新的分子进化模式,即遗传多样性上限理论,重新构建了一个新的人类起源模型。这一模型与多地区起源说基本吻合, 重新把现代人类起源地定位在了东亚。非洲说与东亚说在线粒体进化树上的主要区别是单倍型N和R的关系,非洲起源说认为N是R的祖先,东亚说则反之。本研究引用了已发表的古代人群mtDNA数据,重点分析了线粒体单倍群N和R的关系。结果显示,三个最古老的人类（一个距今45000年,其他两个约40000年）都属于单倍群R;在距今39500到30000年前的人类样本中,绝大部分属于单倍群R下游的亚单倍群U,只有两例为单倍群N（Oase1距今39500年,Salkhit距今34425年）。这两例所属单倍型位于单倍群N下游最基本的未分化亚型,不属于今天存在的任何N下游单倍型,所以可能靠近单倍群N的根部。这些古DNA数据揭示单倍群R比单倍群N古老大约5000年,进一步证实了亚洲起源说的正确性,非洲说的依据不足。     

Origins and divergence times of mammalian class II MHC gene clusters

The class I and II major histocompatibility complex (MHC) genes are apparently subject to evolution by a birth-and-death process. The rate of gene turnover is much slower in the latter genes than in the former. In placental mammals, the class II region can be subdivided into different orthologous subregions or gene clusters (DR, DQ, DO, and DN), but the origins and evolutionary relationships of these gene clusters are not well established. Here we report the results of our study of the times of origin and evolutionary relationships of these gene clusters in mammals. Our analysis suggests that both class II alpha-chain and beta-chain gene clusters are shared by placental mammals and marsupials, but the gene clusters from nonmammalian species are paralogous to mammalian gene clusters. We estimated the times of divergence between gene clusters in placental mammals using the linearized tree and distance regression methods. Our results indicate that most gene clusters originated 170-200 million years (MY) ago, but that DO beta-chain genes diverged from the other beta-chain gene clusters approximately 210-260 MY ago. The phylogenetic trees for the alpha- and beta-chain genes were not congruent, suggesting that the evolutionary history of the class II gene clusters is more complex than previously thought.     

The origin and age of haplochromine fishes in Lake Victoria, east Africa

According to a widely held view, the more than 300 species of haplochromine cichlid fishes in Lake Victoria (LV), East Africa, originated from a single founder species in less than 12,000 years. This view, however, does not follow from the published geological and molecular evidence. The former does indeed suggest that the LV basin dried out less than 15,000 years ago, but it does not provide any information about the species that re-colonized the new lake or that remained in the rivers draining the area. The molecular evidence is inconclusive with respect to the origin of the LV haplochromines because cichlids from critical regions around LV were not adequately sampled; and as far as the age of the LV haplochromines is concerned, it in fact led to an estimate of 250,000-750,000 years old. In the present study, mitochondrial DNA (control region) variation was determined by heteroduplex and sequencing analyses of more than 670 specimens collected at widely distributed East African riverine and lacustrine localities. The analyses revealed the existence of seven haplogroups (I-VII) distinguishable by characteristic substitutions. All endemic LV samples tested fell into one of these haplogroups (V) which, however, was also found to be present at various other localities, both riverine and lacustrine, outside LV. Within this haplogroup, four subgroups (VA through VD) could be distinguished, two of which (VB and VC) were represented in LV and at other localities. The great majority of the LV haplochromine species could be classified as belonging to the VC subgroup, which was found only in LV and in the rivers draining into it. Hence, while the endemic haplochromine species of LV could not have originated from a single founding population, the lake does harbour a large species flock which probably arose in situ.     

Phylogenetic relationships of elapid snakes based on cytochrome b mtDNA sequences

Published molecular phylogenetic studies of elapid snakes agree that the marine and Australo-Melanesian forms are collectively monophyletic. Recent studies, however, disagree on the relationships of the African, American, and Asian forms. To resolve the relationships of the African, American, and Asian species to each other and to the marine/Australo-Melanesian clade, we sequenced the entire cytochrome b gene for 28 elapids; 2 additional elapid sequences from GenBank were also included. This sample includes all African, American, and Asian genera (except for the rare African Pseudohaje), as well as a representative sample of marine/Australo-Melanesian genera. The data were analyzed by the methods of maximum-parsimony and maximum-likelihood. Both types of analyses yielded similar trees, from which the following conclusions can be drawn: (1) Homoroselaps falls outside a clade formed by the remaining elapids; (2) the remaining elapids are divisible into two broad sister clades, the marine/Australo-Melanesian species vs the African, American, and Asian species; (3) American coral snakes cluster with Asian coral snakes; and (4) the "true" cobra genus Naja is probably not monophyletic as the result of excluding such genera as Boulengerina and Paranaja.     

Biogeography and speciation patterns of the golden orb spider genus Nephila (Araneae: Nephilidae) in Asia

The molecular phylogeny of the globally distributed golden orb spider genus Nephila (Nephilidae) was reconstructed to infer its speciation history, with a focus on SE Asian/W Pacific species. Five Asian, two Australian, four African, and one American species were included in the phylogenetic analyses. Other species in Nephilidae, Araneidae, and Tetragnathidae were included to assess their relationships with the genus Nephila, and one species from Uloboridae was used as the outgroup. Phylogenetic trees were reconstructed from one nuclear (18S) and two mitochondrial (COI and 16S) markers. Our molecular phylogeny shows that the widely distributed Asian/Australian species, N. pilipes, and an African species, N. constricta, form a clade that is sister to all other Nephila species. Nested in this Nephila clade are one clade with tropical and subtropical/temperate Asian/Australian species, and the other containing African and American species. The estimated divergence times suggest that diversification events within Nephila occurred during mid-Miocene to Pliocene (16 Mya-2 Mya), and these time periods were characterized by cyclic global warming/cooling events. According to Dispersal and Vicariance Analysis (DIVA), the ancestral range of the Asian/Australian clade was tropical Asia, and the ancestral range of the genus Nephila was either tropical Asia or Africa. We conclude that the speciation of the Asian/Australian Nephila species was driven by Neogene global cyclic climate changes. However, further population level studies comparing diversification patterns of sister species are needed to determine the mode of speciation of these species.     

The phylogeny of the Pantropical genus Arrhipis Bonvouloir (Coleoptera, Eucnemidae)

The phylogeny of the genus Arrhipis Bonvouloir (Coleoptera, Eucnemidae) is clarified with a cladistic analysis based on five molecular markers and morphology. Sixteen species from Africa, America, Asia, and Australia are included in the analysis. Two separate Asian clades are recovered, one of them being the sister group to a clade with the American and African species. With the exception of the continental south-east Asian species, all Gondwanan regions have monophyletic faunas. According to the present data, the continental south-east Asian fauna comprises two monophyletic groups, one of which is the sister group to African and American species. Vicariance seems to be the logical explanation for the distribution of these lignicolous beetles.
© The Willi Hennig Society 2009.     

The historical biogeography of the freshwater knifefishes using mitogenomic approaches: A Mesozoic origin of the Asian notopterids (Actinopterygii: Osteoglossomorpha)

The continental distributions of freshwater fishes in the family Notopteridae (Osteoglossomorpha) across Africa, India, and Southeast Asia constitute a long standing and enigmatic problem of freshwater biogeography. The migrational pathway of the Asian notopterids has been discussed in light of two competing schemes: the first posits recent transcontinental dispersal while the second relies on distributions being shaped by ancient vicariance associated with plate-tectonic events. In this study, we determined complete mitochondrial DNA sequences from 10 osteoglossomorph fishes to estimate phylogenetic relationships using partitioned Bayesian and maximum likelihood methods and divergence dates of the family Notopteridae with a partitioned Bayesian approach. We used six species representing the major lineages of the Notopteridae and seven species from the remaining osteoglossomorph families. Fourteen more-derived teleosts, nine basal actinopterygians, two coelacanths, and one shark were used as outgroups. Phylogenetic analyses indicated that the African and Asian notopterids formed a sister group to each other and that these notopterids were a sister to a clade comprising two African families (Mormyridae and Gymnarchidae). Estimated divergence time between the African and Asian notopterids dated back to the early Cretaceous when India–Madagascar separated from the African part of Gondwanaland. Thus, estimated time of divergence based on the molecular evidence is at odds with the recent dispersal model. It can be reconciled with the geological and paleontological evidence to support the vicariance model in which the Asian notopterids diverged from the African notopterids in Gondwanaland and migrated into Eurasia on the Indian subcontinent from the Cretaceous to the Tertiary. However, we could not exclude an alternative explanation that the African and Asian notopterids diverged in Pangea before its complete separation into Laurasia and Gondwanaland, to which these two lineages were later confined, respectively.