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PubMed2000

Batrachology of Japan and adjacent regions - a systematic review.

As is the case with most other organisms, studies of amphibians started with systematics as the basis for many other biological fields, but systematics itself has endured a slower progress than other fields of biology have enjoyed for a long time. Nevertheless, philosophical and methodological 'revolutions' in the past 30 years, combined with more recent progress in biochemical and molecular techniques, have been forcing current systematics into a great change. Stejneger's (1907) monumental book, the first thorough review of amphibians from Japan and adjacent regions, was published nearly a century ago, and since then, the increase in number of areas that have been closely surveyed, together with the application of new theories and methods, have greatly enlarged our knowledge of the amphibian fauna in this region. For example, extensive experiments by the Hiroshima School using artificial hybridization techniques greatly contributed to our understandings of relationships among some groups of amphibians that had been taxonomically confusing. In addition to this, new species discovered by more detailed field surveys in a wider area and cryptic species revealed by analyses of isozymes and acoustic properties have made for a great increment in the number of taxa in this region. Further, analyses of DNA sequences now enable us to infer the affinities of taxa with few phylogenetically informative phenotypic properties, and the resultant phylogenetic hypotheses further contribute to our understandings of biogeography and many other issues on amphibian evolution. From these advances, it has been clarified that the amphibian species diversity is far greater than was previously expected, which in turn means a high endemism within particular regions. It is expected that future studies will also reveal exact systematic relationships of wide-ranging species, both those occurring within this region and those extending outside of it. For that purpose, international and interdisciplinary studies are indispensable. But what is also necessary is to conserve amphibian populations so that they will not disappear before their true relationships are realized. Knowledge of systematics among young amphibian biologists is also a matter of high priority.

Amphibians↗
PubMed2003

Evolution of low-copy number and major satellite DNA sequences coexisting in two Pimelia species-groups (Coleoptera).

Satellite DNA sequence evolution has been studied in several insect species from the genus Pimelia (Tenebrionidae, Coleoptera). Low-copy number homologs of the previously characterized major satellite DNA from P. monticola (PMON) have been cloned and sequenced from six congeneric species belonging to two species groups: Ibero-Balearic and Moroccan. Sequence analysis of a sample of low-copy number repeats revealed two subfamilies, differing on average 17.5% due to randomly spread single point mutations. Each subfamily is specific for a group of taxa in congruence with their biogeography. Within each group, there is no significant species-specific clustering of the sequences. These results suggest that the two satellite subfamilies arose after the split of an ancestral lineage into the North African and Ibero-Balearic Pimelia species-groups, but before their subsequent radiation. Rate heterogeneity tests suggest that PMON sequences have evolved faster in the lineage leading to the Moroccan group. Comparison of sequence divergences between minor PMON and the previously characterized major PIM357 satellite obtained from the same taxa, points to similar evolutionary dynamics. Both sequences are evolving in parallel accumulating mutations in a gradual manner irrespectively of significant differences in abundance. These data show that copy number of the sequence families does not necessarily affect the sequence change dynamics of satellite repeats.

Animals↗
PubMed1998

[Molecular systematics of Phlebotominae: a pilot study. Paraphyly of the genus Phlebotomus].

Phylogenetic relationships among Phlebotominae were inferred through a pilot study using parsimony analysis of the D2 domain of ribosomal DNA sequences: 455 pairs of bases were sequenced in nine species of Phlebotomine sandflies which belong to the genera Lutzomyia, Phlebotomus and Sergentomyia. Two taxa are used as outgroups: Psychoda sp. and Nemapalpus flavus which is the sister group of the Phlebotominae. The South American genus Lutzomyia appears to be monophyletic. The Mediterranean species Sergentomyia dentata is its sister group and is not clustered with the Old World genus Phlebotomus. The latter is a paraphyletic genus with an early individualization of the branch including the closely related subgenera Phlebotomus and Paraphlebotomus, and a late individualization of the subgenus Larroussius. These results have some consequences on the biogeography of the leishmaniasis in the Old World.

Animals↗
PubMed1998

Early mammals: teeth, jaws and finally a skeleton!

Suprising new fossils - a skeleton and a jaw - give us a much clearer picture of mammals that lived during the time of non-avian dinosaurs; the new finds illuminate the early evolution of the lineage leading to modern mammals, and challenge traditional understanding of placental mammal evolution and biogeography.

Animals↗
PubMed2002

The Atlas mountains as a biogeographical divide in North-West Africa: evidence from mtDNA evolution in the Agamid lizard Agama impalearis.

Since the early Miocene there have been several physical events within NW Africa that are likely to have had a major impact on its faunal diversity. Phylogeographical studies will shed new light on the biogeography of the region. We analysed mitochondrial DNA diversity in the agamid lizard Agama impalearis (also called A. bibronii) based on sequences from mitochondrial genes with very different evolutionary rates (16S rRNA and ND2). Well-supported topologies of rooted maximum parsimony trees (with a Laudakia outgroup) and unrooted haplotype networks indicated two major clades with similar branch lengths. These clades have non-overlapping distributions representing respective areas to the North and West and South and East of the Atlas mountain chain and each could be given full species recognition. Nested clade analyses indicate that historical and possible present-day allopatry account for the primary phylogeographic pattern. Further evidence is provided by the estimated timing of cladogenesis, based on calibration of evolutionary rates in the ND2 gene of another continental Agamid. Sequence divergence between clades corresponds to 8.5-9.4mya, coinciding with the main period of orogenic uplift of the Atlas. Additional evidence of cladogenesis by allopatric fragmentation is also detected within the North/West Atlas clade, although contiguous range expansion is the most predominant explanation of more recent phylogeographic effects in this species. Miocene vicariance mediated by the Atlas may provide a general explanation of intra- and interspecific biogeographical patterns in NW African species.

Africa, Northern↗
PubMed2003

Chloroplast and nuclear evidence for multiple origins of polyploids and diploids of Hedera (Araliaceae) in the Mediterranean basin.

Chloroplast (trnT-L) and nuclear rDNA (ITS) sequence analyses of the Araliaceae provide strong molecular evidence for the monophyly of the genus Hedera. Phylogenetic reconstructions suggest multiple origins and an active polyploidization process not only in the formation of tetraploids (2n = 96), hexaploids (2n = 144), and octoploids (2n = 192), but also of diploids (2n = 48). A high basic chromosome number of x = 24, extensive polyphyly in widespread diploids, and terminal placement of Hedera in phylogenies of the Araliaceae reveal that extant diploid taxa may be, in fact, assemblages of ancestral polyploids from plants of n = 12. Four major lineages containing four types of chloroplast (chlorotypes I, II, III, and IV), which are defined by different trnT-L nucleotide substitutions and two large insertions (50- and 30-bp), provide evidence for evolutionary processes and historical biogeography in Hedera. We propose a scenario where an initial colonization in the Mediterranean basin by Asian ancestors (carrying the ancestral Araliaceae chlorotype I) is followed by differentiation into the four chlorotypes of the Mediterranean region, and then recolonization of Asia and northern Europe only by chlorotype III. The Macaronesian taxa (Hedera azorica, Hedera maderensis ssp. maderensis, and Hedera canariensis) appear to have originated from a single-colonization event to each archipelago with no further contact either with continental or insular species.

Base Sequence↗
PubMed2003

Monophyly and relationships of the tribe Exaceae (Gentianaceae) inferred from nuclear ribosomal and chloroplast DNA sequences.

Both chloroplast trnL (UAA) intron and nuclear ribosomal ITS sequences highly confirmed the monophyly of the tribes of the Gentianaceae defined by the recent classification, and revealed the tribe Exaceae as a basal clade just next to the basal-most lineage, the tribe Saccifolieae. Within the tribe Exaceae, Sebaea (except Sebaea madagascariensis) appeared as the most basal clade as the sister group to the rest of the tribe. The Madagascan endemic genera Gentianothamnus and Tachiadenus were very closely related to each other, together standing as sister to a clade comprising Sebaea madagascariensis, Ornichia, and Exacum. The saprophytic genus Cotylanthera nested deeply inside Exacum. Sebaea madagascariensis was shown closer to the Madagascan endemic genus Ornichia than to any other sampled Sebaea species. Exacum appeared as the most derived taxon within this tribe. The topology of the phylogenetic trees conform with the Gondwana vicariance hypothesis regarding the biogeography of Exaceae. However, no evidence for matching the older relationships within the family to the tectonic history could be corroborated with various divergence time analyses. Divergence dating estimated a post-Gondwana diverging of the Gentianaceae about 50 million years ago (MYA), and the tribe Exaceae as about 40 MYA. The Mozambique Channel land-bridge could have played an important role in the biogeographic history of the tribe Exaceae.

Africa↗
PubMed2003

Evolutionary and biogeographical patterns within Iberian populations of the genus Squalius inferred from molecular data.

Origins and biogeography of the chub, genus Squalius (formerly within the genus Leuciscus), in the Iberian Peninsula were inferred from comparison between patterns of geographic distribution and phylogenetic relationships among populations belonging to 14 European Squalius species. The phylogeny recovered was based on the complete sequence of the mitochondrial cytochrome b gene. Squalius species were grouped into three major clades. The basal clade included species distributed across the ancient Paratethys Sea. The second clade included species from Central and East Europe and the northern areas of the Mediterranean basin towards Minor Asia. The third clade included species from the Mediterranean Peninsulas (Iberian, Italy, and Balkans). The Iberian Squalius species do not constitutes a monophyletic group. Our data indicate that the Iberian Peninsula was colonized at least twice by two different monophyletic lineages, a meridional group and a Central Europe group. The amount of species diversity found in the Iberian Peninsula and the phylogenetic relationships among these species, together with their geographic distribution, suggest that the Central Europe lineage colonized the Iberian Peninsula at a latter time. Our data indicate that the northeastern Iberian lineage is phylogenetically close to Greek populations of Squalius cephalus, while the second lineage formed a monophyletic group including Squalius pyrenaicus, Squalius carolitertii, Squalius aradensis, and Squalius torgalensis. The speciation process that generated these species and the geographic structure of their populations, principally in S. pyrenaicus, can be attributed to paleogeographical events like the ancient endorrheism and the development of hydrographic basins.

Animals↗
PubMed2003

Phylogeny of magpies (genus Pica) inferred from mtDNA data.

We investigated the phylogenetic relationships of species and subspecies of the cosmopolitan genus Pica using 813 bp of the mitochondrial genome (including portions of 16s rDNA, tRNA-Leu, and ND1). The phylogenetic relationships within the genus Pica revealed in our molecular analyses can be summarized as follows: (1). the Korean magpie (Pica pica sericea) appears basal within the genus Pica; (2). the European magpie (Pica pica pica) shows a close relationship to the Kamchatkan magpie (Pica pica camtschatica); (3). two North American species (Pica hudsonia and Pica nuttalli) shows a sister-group relationship; (4). most importantly, the European+Kamchatkan clade appears more closely related to the North American clade than to Korean magpies. Based on these results and genetic distance data, it is possible that members of an ancestral magpie lineage in East Asia initially moved north to form Kamchatkan magpies and then crossed the Bering land bridge to found North American taxa. At a later date, a group might have split off from Kamchatkan magpies and migrated west to form the Eurasian subspecies. The divergence between the two North American taxa appears to have happened no later than the divergence of Eurasian subspecies and both processes appear to have been relatively rapid. Rather than the formation of P. hudsonia by re-colonization from an Asian magpie ancestor, as suggested by, our data suggest a shared ancestry between P. hudsonia and P. nuttalli. Based on the above findings, including phylogenetic placement of P. hudsonia and P. nuttalli as nested within the larger Pica pica clade, and the lack of evidence suggesting reproductive isolation within the genus Pica, we believe that the current classification may be inaccurate. A more conservative classification would recognize one monophyletic species (i.e., P. pica) and treat P. nuttalli and P. hudsonia as subspecies (i.e., P. p. nuttalli and P. p. hudsonia). More extensive studies on the population genetics and biogeography of magpies should be conducted to better inform any taxonomic decisions.

Animals↗
PubMed2003

A new phylogenetic marker, apolipoprotein B, provides compelling evidence for eutherian relationships.

Higher-level relationships within, and the root of Placentalia, remain contentious issues. Resolution of the placental tree is important to the choice of mammalian genome projects and model organisms, as well as for understanding the biogeography of the eutherian radiation. We present phylogenetic analyses of 63 species representing all extant eutherian mammal orders for a new molecular phylogenetic marker, a 1.3kb portion of exon 26 of the apolipoprotein B (APOB) gene. In addition, we analyzed a multigene concatenation that included APOB sequences and a previously published data set (Murphy et al., 2001b) of three mitochondrial and 19 nuclear genes, resulting in an alignment of over 17kb for 42 placentals and two marsupials. Due to computational difficulties, previous maximum likelihood analyses of large, multigene concatenations for placental mammals have used quartet puzzling, less complex models of sequence evolution, or phylogenetic constraints to approximate a full maximum likelihood bootstrap. Here, we utilize a Unix load sharing facility to perform maximum likelihood bootstrap analyses for both the APOB and concatenated data sets with a GTR+Gamma+I model of sequence evolution, tree-bisection and reconnection branch-swapping, and no phylogenetic constraints. Maximum likelihood and Bayesian analyses of both data sets provide support for the superordinal clades Boreoeutheria, Euarchontoglires, Laurasiatheria, Xenarthra, Afrotheria, and Ostentoria (pangolins+carnivores), as well as for the monophyly of the orders Eulipotyphla, Primates, and Rodentia, all of which have recently been questioned. Both data sets recovered an association of Hippopotamidae and Cetacea within Cetartiodactyla, as well as hedgehog and shrew within Eulipotyphla. APOB showed strong support for an association of tarsier and Anthropoidea within Primates. Parsimony, maximum likelihood and Bayesian analyses with both data sets placed Afrotheria at the base of the placental radiation. Statistical tests that employed APOB to examine a priori hypotheses for the root of the placental tree rejected rooting on myomorphs and hedgehog, but did not discriminate between rooting at the base of Afrotheria, at the base of Xenarthra, or between Atlantogenata (Xenarthra+Afrotheria) and Boreoeutheria. An orthologous deletion of 363bp in the aligned APOB sequences proved phylogenetically informative for the grouping of the order Carnivora with the order Pholidota into the superordinal clade Ostentoria. A smaller deletion of 237-246bp was diagnostic of the superordinal clade Afrotheria.

Amino Acid Sequence↗
PubMed2003

Two Corbicula (Corbiculidae: Bivalvia) mitochondrial lineages are widely distributed in Asian freshwater environment.

We investigated the biogeography of Asian Corbicula using mitochondrial gene sequence variation for Corbicula members sampled from 24 localities of eight Asian regions. A total of 210 individuals were genetically characterized by examining sequence variations of a 614 bp fragment of the mitochondrial cytochrome oxidase I (COI) gene. Phylogenetic analyses of the COI dataset revealed that Corbicula members are subdivided into two well-supported clades: estuarine and freshwater. A robust dichotomy between the Japanese/Korean (Corbicula japonica) and Chinese (Corbicula fluminalis) estuarine forms was evident, suggesting that these two regional populations represent a deep phylogeographic split. Our mitochondrial gene tree showed that among the freshwater members, two Corbicula mitochondrial lineages are the most common, having attained extensive geographic distribution in the Asian freshwater environment. While the present study provides significant biogeographic information on Asian Corbicula, a comprehensive phylogenetic study by cross-referencing the mitochondrial-based Corbicula phylogeny with nuclear gene data is required to fully understand the evolutionary origin(s) of triploidy/clonality in this genus.

Animals↗
PubMed2004

Molecular phylogeny of Lysimachia (Myrsinaceae) based on chloroplast trnL-F and nuclear ribosomal ITS sequences.

Both nuclear ribosomal ITS and chloroplast trnL-F sequences were acquired for 57 species (accessions) of Lysimachia and its close relatives, and were analyzed together with sequences retrieved from databases. The results of phylogenetic analyses based on these data (separately or combined) show that Lysimachia is paraphyletic, with the monotypic genus Glaux nested deeply inside. Previous suggestions that Anagallis and Trientalis could be ingroups of Lysimachia were not corroborated by our results. The molecular phylogenies do not support the current infrageneric divisions of Lysimachia. Subgenus Lysimachia contains at least five independent lineages. The Hawaii endemic subgenus Lysimachiopsis was shown to group with subgenera Palladia and Heterostylandra, instead of subgenus Idiophyton as previously suggested. The two North American representatives of Lysimachia, subgenus Seleucia and section Verticillatae of subgenus Lysimachia are group together as the most basal clade of the genus. Parallel and independent evolutions were inferred for morphological characters that were previously used as diagnostic criteria. Molecular phylogenies do not offer clear inferences on the overall historical biogeography of Lysimachia, but Southeast Asia origins of several clades, including the Hawaiian endemic clade and the Iberian Lysimachia ephemerum are strongly supported.

Cell Nucleus↗
PubMed2002

Mitochondrial genomes of parasitic flatworms.

Complete or near-complete mitochondrial genomes are now available for 11 species or strains of parasitic flatworms belonging to the Trematoda and the Cestoda. The organization of these genomes is not strikingly different from those of other eumetazoans, although one gene (atp8) commonly found in other phyla is absent from flatworms. The gene order in most flatworms has similarities to those seen in higher protostomes such as annelids. However, the gene order has been drastically altered in Schistosoma mansoni, which obscures this possible relationship. Among the sequenced taxa, base composition varies considerably, creating potential difficulties for phylogeny reconstruction. Long non-coding regions are present in all taxa, but these vary in length from only a few hundred to approximately 10000 nucleotides. Among Schistosoma spp., the long non-coding regions are rich in repeats and length variation among individuals is known. Data from mitochondrial genomes are valuable for studies on species identification, phylogenies and biogeography.

Animals↗
PubMed2002

Phylogeography of the neotropical sand fly Lutzomyia longipalpis inferred from mitochondrial DNA sequences.

Sand flies in the Lutzomyia longipalpis species complex include the primary vector of Leishmania chagasi, the etiologic agent of visceral leishmaniasis in the Neotropics. Twelve L. longipalpis populations from South and Central America were compared using the cytochrome c oxidase I (COI) gene from the mitochondrial genome. The haplotype profiles for each population revealed that the majority of sequence variation was inter-population (98%) rather than intra-population, suggesting that sequence polymorphisms at the COI locus should provide excellent characters for the study of phylogenetic relationships among populations. Phylogenetic reconstruction using distance (neighbor-joining) and maximum parsimony analysis revealed the existence of four clades among the L. longipalpis populations studied: (1) Laran, (2) Brazilian, (3) cis-Andean and (4) trans-Andean. We suggest that these clades represent species. A biogeographical interpretation of the molecular phylogeny suggests that the process of speciation in the L. longipalpis complex began in the Pliocene, from a sub-Andean-Amazonian gene pool resulting from the Andean orogeny (formation of the East Andean Cordillera). The four clades probably diverged as a result of vicariance events that occurred throughout the late Pliocene and Pleistocene. We propose and discuss several historical scenarios, based on the biogeography and historical geology of Central and South America.

Animals↗
PubMed2003

The phylogeny of the Schistosomatidae based on three genes with emphasis on the interrelationships of Schistosoma Weinland, 1858.

Schistosomes are digenean flukes, parasitic of birds, mammals and crocodiles. The family Schistosomatidae contains species of considerable medical and veterinary importance, which cause the disease schistosomiasis. Previous studies, both morphological and molecular, which have provided a good deal of information on the phylogenetics of this group, have been limited in the number of species investigated or the type or extent of molecular data used. This paper presents the most comprehensive phylogeny to date, based on the sequences of 3 genes, complete ribosomal small subunit rRNA and large ribosomal subunit rRNA, and mitochondrial cytochrome oxidase 1, sequenced from 30 taxa including at least 1 representative from 10 of the 13 known genera of the Schistosomatidae and 17 of the 20 recognized Schistosoma species. The phylogeny is examined using morphological characters, intermediate and definitive host associations and biogeography. Theories as to the origins and spread of Schistosoma are also explored. The principal findings are that Ornithobilharzia and Austrobilharzia form a sister group to the Schistosoma; mammalian schistosomes appear paraphyletic and 2 Trichobilharzia species, T. ocellata and T. szidati, seem to be synonymous. The position of Orientobilharzia within the Schistosoma is confirmed, as is an Asian origin for the Schistosoma, followed by subsequent dispersal through India and Africa.

Animals↗
PubMed2004

Anaplasma marginale (Rickettsiales: Anaplasmataceae): recent advances in defining host-pathogen adaptations of a tick-borne rickettsia.

The tick-borne intracellular pathogen Anaplasma marginale (Rickettsiales: Anaplasmataceae) develops persistent infections in cattle and tick hosts. While erythrocytes appear to be the only site of infection in cattle, A. marginale undergoes a complex developmental cycle in ticks and transmission occurs via salivary glands during feeding. Many geographic isolates occur that vary in genotype, antigenic composition, morphology and infectivity for ticks. In this chapter we review recent research on the host-vector-pathogen interactions of A. marginale. Major surface proteins (MSPs) play a crucial role in the interaction of A. marginale with host cells. The MSP1a protein, which is an adhesin for bovine erythrocytes and tick cells, is differentially regulated and affects infection and transmission of A. marginale by Dermacentor spp. ticks. MSP2 undergoes antigenic variation and selection in cattle and ticks, and contributes to the maintenance of persistent infections. Phylogenetic studies of A. marginale geographic isolates using msp4 and msp1alpha provide information about the biogeography and evolution of A. marginale: msp1alpha genotypes evolve under positive selection pressure. Isolates of A. marginale are maintained by independent transmission events and a mechanism of infection exclusion in cattle and ticks allows for only the infection of one isolate per animal. Prospects for development of control strategies by use of pathogen and tick-derived antigens are discussed. The A. marginale/vector/host studies described herein could serve as a model for research on other tick-borne rickettsiae.

Anaplasma marginale↗
PubMed2005

Phylogeny, evolution and host-parasite relationships of the order Proteocephalidea (Eucestoda) as revealed by combined analysis and secondary structure characters.

In a manner similar to many other groups of organisms, the tapeworm order Proteocephalidea poses a difficult phylogenetic problem if treated on the basis of single-gene analysis. Since the biogeography and host distribution of proteocephalideans make these tapeworms a potentially interesting model for evolutionary and co-evolutionary studies, we tried to resolve their phylogenetic relationships by applying a multi-gene approach. The ITS2 sequences and V4 hypervariable loop of 18S rRNA were obtained for 43 and 35 proteocephalidean taxa, respectively, and combined with other sequences available in the GenBank. The phylogenetic analysis of the combined DNA set was confronted with characters derived from ITS2 secondary structures. Using this approach, a species-rich Neotropical lineage of proteocephalideans could be reliably resolved. The phylogenetic relationships within this group show a high degree of phylogeny-independent host distribution. The reconstruction of ITS2 secondary structure revealed a universal 4-domain arrangement, which is conserved across a wide range of Neodermata. Several motifs of the secondary structure could be mapped to the phylogenetic tree as possible clade synapomorphies.

Animals↗
PubMed2006

Towards a unified science of cultural evolution.

We suggest that human culture exhibits key Darwinian evolutionary properties, and argue that the structure of a science of cultural evolution should share fundamental features with the structure of the science of biological evolution. This latter claim is tested by outlining the methods and approaches employed by the principal subdisciplines of evolutionary biology and assessing whether there is an existing or potential corresponding approach to the study of cultural evolution. Existing approaches within anthropology and archaeology demonstrate a good match with the macroevolutionary methods of systematics, paleobiology, and biogeography, whereas mathematical models derived from population genetics have been successfully developed to study cultural microevolution. Much potential exists for experimental simulations and field studies of cultural microevolution, where there are opportunities to borrow further methods and hypotheses from biology. Potential also exists for the cultural equivalent of molecular genetics in "social cognitive neuroscience," although many fundamental issues have yet to be resolved. It is argued that studying culture within a unifying evolutionary framework has the potential to integrate a number of separate disciplines within the social sciences.

Animals↗