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At least 397 records · Page 22Linked to original sources
PubMed1997

Repetitive DNA sequences as an insight into Aeglidae (Crustacea, Anomura) evolution.

The evolutionary relationships of five Atlantic Aeglidae species (Aegla neuquensis affinis, A. humahuaca, A. jujuyana, A. platensis, and A. uruguayana) were studied by (i) satellite DNA analysis using a restriction enzyme digestion and hybridization pattern approach and (ii) genome screening by using randomly amplified polymorphic DNA (RAPD) typing. The identical restriction patterns and intense interspecific hybridization patterns obtained in this study strongly suggest a recent cladogenetic event for the Aeglidae. The species-specific amplification products which were detected using RAPD markers allowed species characterization. A total of 49 amplification products were used to construct trees by cluster analysis. The new scheme agrees in part with previous proposals based on biogeography and morphology. We considered that the subdivision northwestern-platensis species was probably due to the rising of the Andes, which started in the Middle Miocene. Divergence due to altitude is suggested by the different altitudinal distribution of three northwestern species along the same river. The possible role of selection by ecological factor/s was observed at the population level in A. jujuyana, which has a wider altitudinal range distribution. RAPD markers revealed a high level of intraspecific diversity and important genetic flow among populations. However, a few markers showed significant differences in frequency or H between the lowermost population and the other populations, located in a different biogeographical region. The differences were not in relation to geographical distance, and we interpreted them as being due to selection. Repetitive sequences constitute an important reservoir of genetic variation, and these results show their usefulness in testing and proposing evolutionary hypothesis in crabs. These sequences seem to have played an important role in aeglid evolution. Ecological factors related to altitude have probably influenced macro- and microevolutionary processes, at least in northwestern species.

Animals↗
PubMed2001

Onchocerca volvulus: genetic diversity of parasite isolates from Sudan.

Onchocerciasis in Sudan exists in three distinct foci which exhibit differing clinical presentations. Previous studies have demonstrated that a tandemly repeated Onchocerca sequence family with a unit repeat length of 150 bp (the O-150 family) is a useful marker for deducing relationships among different O. volvulus populations. In the current study, the O-150 repeat families of O. volvulus from Sudan were analyzed and compared to each other and to those of parasites from West Africa. Similar to West African and American O. volvulus, the O-150 families of the Sudanese parasites could be divided into clusters within which little or no intracluster variation was evident, suggesting that the O-150 family in these parasites was subject to the forces of concerted evolution. Statistical analysis of the O-150 families from the different Sudanese parasite isolates, employing a nested algorithm based on an analysis of variance, revealed that O. volvulus endemic to the northern focus at Abu Hamed were significantly different from all other O. volvulus populations examined to date. In contrast, parasites from the southern and eastern foci of Sudan were indistinguishable from those endemic to the West African savanna. The significance of these data are discussed in light of knowledge of the biogeography and biology of transmission of O. volvulus in Africa.

Africa, Western↗
PubMed1995

Saltationist and punctuated equilibrium models for the evolution of viviparity and placentation.

Vertebrate viviparity (live-bearing reproduction), placentation, and placentotrophy are widely assumed to have evolved as three successive, gradualistic transformations. From empirical data and predictive tests on lizards and snakes, this paper indicates that placentae and a degree of placentotrophy have evolved repeatedly as necessary correlates of viviparity, not as subsequent modifications. In addition, information derived from studies of anatomy, physiology, biogeography and systematics is used to evaluate new saltationist and punctuated equilibrium models for the evolution of viviparity. Phylogenetic reconstruction reveals that more than 100 squamate clades have made the transition to viviparity and placentation. However, various phenotypic intermediates postulated by the gradualistic model are either scarce or unrepresented among known forms, including those in which viviparity has evolved at specific and subspecific levels. Evolution in squamates seems to have produced a dichotomy between two evolutionarily stable patterns: (i) retention of weakly shelled or shell-free eggs to term (viviparity), with development of fully functional placentae; and (ii) deposition of shelled eggs at or near the limb bud stage of development (typical oviparity). Conflicting functional demands placed on eggshell morphology may constrain establishment of prolonged, oviparous egg-retention as a viable, historically stable pattern. Alternatively, the costs of prolonged egg-retention associated with decreased female mobility or decreased fecundity may exceed the benefits in oviparous forms.

Animals↗
PubMed2001

Spatial heterogeneity and critical patch size: Area effects via diffusion in closed environments.

We describe a class of mathematical models for critical patch size in which the mechanisms inducing area effects are based on source-sink population dynamics arising from dispersal throughout a closed, finite, but spatially heterogeneous environment. Our models are reaction-diffusion equations, but unlike classical KISS models for area effects they do not assume that there is dispersal across the boundary of the environment into a hostile exterior. We observe that simple rescaling has the same effects in our models as in KISS models and hence predicts the same sort of area effects, but that other sorts of rescaling may not predict area effects. The models considered here provide an alternative to the KISS models used in our previous work on species-area relationships in island biogeography.

Animals↗
PubMed1995

MtDNA phylogeography of the California newt, Taricha torosa (Caudata, Salamandridae).

Thirty-six individuals of the California newt, Taricha torosa, representing 22 populations from throughout the range of the two currently recognized subspecies, torosa and sierrae, were examined for sequence variation in a segment (375 bp) of the mitochondrial (mt) cytochrome b gene. The maximum sequence divergence within T. torosa is about 9%. Phylogenetic analyses used the sister taxa T. rivularis and T. granulosa as outgroups. Eighteen haploid sequence types found in T. torosa were grouped by parsimony, maximum likelihood, and neighbor-joining analyses into five mitochondrial clusters: two in torosa (the northern and southern clusters) and three in sierrae (the northern, central, and southern clusters). The southern sierrae cluster apparently shared a most recent common ancestor with the northern torosa cluster. The approximate time of sequence divergence within the current species was calibrated using the known fossil record (0.8% divergence per million years or 0.01 maximum likelihood distance per million years). Phylogenetic implications of mtDNA sequence variation for evolution and biogeography of the T. torosa species complex are discussed.

Amino Acid Sequence↗
PubMed1996

A phylogeny for the African treefrog family Hyperoliidae based on mitochondrial rDNA.

Mitochondrial 12S rRNA sequences were used to construct a phylogeny for the African treefrog family, Hyperoliidae. The sequences were aligned using the well-established mt 12S rRNA secondary structure as a map to designate stem and loop positions. Conservation of secondary structure permits a more accurate basis for assessing homologies than does primary sequence alone. The molecular trees showed many similarities to the morphological trees constructed previously. Species within a genus always grouped together. The genera Hyperolius, Heterixalus, Afrixalus, and Kassina were resolved, but not with statistical significance. Leptopelis was the basal group. The analysis shows clearly that Phylyctimantis groups with Kassina as it did in Drewes' morphological tree and that Tachycnemis groups closely with Heterisxalus, a relationship not suggested by the morphological data. Character weighting (including compensatory base changes), mitochondrial trees vs gene trees, and the biogeography of the group are discussed.

Africa↗
PubMed1996

Molecular phylogenetics of honey bee subspecies (Apis mellifera L.) inferred from mitochondrial DNA sequence.

A mitochondrial DNA region encompassing part of the NADH dehydrogenase subunit 2 and isoleucine transfer RNA genes was PCR amplified, cloned, and sequenced for 14 morphometrically identified Apis mellifera subspecies and the New World "Africanized" honeybee. Twenty different haplotypes were detected and phylogenetic analyses supported the existence of 3 or 4 major subspecies groups similar to those based on morphometric measurements. However, some discrepancies are reported concerning the subspecies composition of each group. Based on the sequence divergence of Drosophila (2% per Myr) we found that the four lineages may have diverged around 0.67 Myr. The variability found in this region enables us to infer phylogenetic relationships and test hypotheses concerning subspecies origin, dispersion, and biogeography.

Africa↗
PubMed1998

Two nuclear genes yield concordant relationships within Attacini (Lepidoptera: Saturniidae).

To extend initial characterizations of their phylogenetic utility, sequences from the nuclear genes for elongation factor-1 alpha (EF-1 alpha) and dopa decarboxylase (DDC) are tested for phylogenetic concordance with each other and with previous morphological evidence within the giant silk moth tribe Attacini (Lepidoptera: Saturniidae). The sampling of DDC is expanded from the 690 basepairs of previous studies to 1051 basepairs in the current study. All nine attacine genera are sampled. EF-1 alpha and DDC agree in the placement of seven of nine genera, with placement of the other two not in strong conflict. Combination of the gene sequences results in a nearly fully resolved tree that is consistent with EF-1 alpha alone and agrees with morphology in five of eight groups. Conflict between molecules and morphology is confined to deeper-level relationships within Attacini, where node support for the molecular hypotheses, but not the morphological hypotheses, is generally very strong. A strong signal is contributed by synonymous substitutions in both genes, and by nonsynonymous change particularly in DDC. The molecular phylogeny supports a revision of attacine biogeography in that neither East Asian nor New World genera form monophyletic groups.

Animals↗
PubMed1999

Polyphyly and convergent morphological evolution in Commelinales and Commelinidae: evidence from rbcL sequence data.

Phylogenetic relationships of the five families of the order Commelinales remain an area of deep uncertainty in higher-level monocot systematics, despite intensive morphological and anatomical study. To test the monophyly of the Commelinales and the subclass Commelinidae, evaluate their relationships, and analyze evolutionary trends in their morphology, ecology, and biogeography, we conducted parsimony analyses on 95 rbcL sequences representing 17 taxa of Commelinales, 16 taxa of other Commelinidae, and 63 taxa from Arecidae, Liliidae, and Zingiberidae. Commelinales is polyphyletic and Commelinidae paraphyletic, with Eriocaulaceae and Xyridaceae sister to Poaceae and its relatives, Rapateaceae sister to Bromeliaceae and Mayacaceae, and Commelinaceae sister to Philydrales and allies. Thurnia is sister to Prionium at the base of Cyperaceae-Juncaceae; only 1 of Cronquist's multifamily commelinoid orders is diagnosed as monophyletic. We propose a revised Commelinidae, incorporating 4 revised superorders (Bromelianae, Commelinanae, Dasypogonanae, Arecanae) and 10 orders ((Poales, Eriocaulales, Cyperales, Typhales, Bromeliales), (Commelinales, Philydrales, Zingiberales), (Dasypogonales), (Arecales)). Morphological and anatomical characters used to define the original Commelinales and Commelinidae appear to be plesiomorphic or to reflect convergence or recurrent mutation; several characters supporting our revised classification are anatomical traits that seem relatively insulated from environmental selection pressures. The Commelinidae distal to the Arecales arose in South America, with amphiatlantic Bromeliaceae-Mayacaceae-Rapateaceae originating in the Guayana Shield. Ecological diversification involved the repeated invasion of shady, infertile, or arid microsites. The numbers of species in families of the revised Commelinidae are related partly to the extent of adaptive radiation in those families, but seem more strongly related to nonadaptive features promoting speciation, such as restricted seed dispersal (especially in forest interior groups with fleshy fruits), polyploidy, aneuploidy, and apomixis. Species diversity is unrelated to the rate/amount of rbcL sequence evolution.

DNA, Plant↗
PubMed1999

Miocene radiation of deep-sea hydrothermal vent shrimp (Caridea: Bresiliidae): evidence from mitochondrial cytochrome oxidase subunit I.

The evolutionary history of deep-sea shrimp (Caridea: Bresiliidae) inhabiting deep-sea hydrothermal vent and hydrocarbon seep environments was assessed using the mitochondrial Cytochrome c Oxidase subunit I (COI) gene (600 bp). Phylogenetic analyses (parsimony, likelihood, and neighbor-joining) recovered three distinct clades (A, Rimicaris/Chorocaris/Opaepele; B, Alvinocaris; and C, Mirocaris) consistent with higher level taxonomy based on morphology. However, robust phylogenetic results suggested that Chorocaris is paraphyletic and that Mirocaris fortunata and M. keldyshi may not be genetically distinct. A Kishino-Hasegawa likelihood approach was used to test alternative phylogenetic hypotheses based on biogeography and morphology. Evolutionary relationships of vent-endemic shrimp species did not appear to be correlated either with their extant biogeographic distribution or with the history of sea floor spreading. Additionally, COI data suggested that these vent-endemic organisms are not remnants of a Mesozoic vent assemblage; instead, they radiated in the Miocene.

Animals↗
PubMed1999

Phylogeny of the Neotropical killifish family Rivulidae (Cyprinodontiformes, Aplocheiloidei) inferred from mitochondrial DNA sequences.

Phylogenetic relationships of 70 taxa representing 68 species of the Neotropical killifish family Rivulidae were derived from analysis of 1516 nucleotides sampled from four different segments of the mitochondrial genome: 12S rRNA, 16S rRNA, cytochrome oxidase I, and cytochrome b. The basal bifurcation of Cynolebiatinae and Rivulinae (Costa, 1990a,b) is supported; however, Terranatos, Maratecoara, and Plesiolebias are rivulins, not cynolebiatins. These three genera, along with the other recognized annual rivulin genera, form a monophyletic clade. Austrofundulus, Rachovia, Renova, Terranatos, and 3 species of the genus Pterolebias, all from northeastern South America, form a monophyletic clade excluding other species of Pterolebias. Pterolebias as presently understood is clearly polyphyletic. Trigonectes and Moema are supported as sister groups but do not form a monophyletic group with the genera Neofundulus and Renova as previously proposed. The suite of adaptations necessary for an annual life history has clearly been lost several times in the course of rivulid evolution. Also revealed is a considerable increase in substitution rate in most annual lineages relative to the nonannual Rivulus species. The widespread and speciose genus Rivulus is paraphyletic, representing both basal and terminal clades within the Rivulidae. Previous hypotheses regarding the vicariant origin of Greater Antillean Rivulus species are supported. Most rivulid clades show considerable endemism; thus, detailed analysis of rivulid phylogeny and distribution will contribute robust hypotheses to the clarification of Neotropical biogeography.

Amino Acid Sequence↗
PubMed2001

A molecular phylogeny of Costaceae (Zingiberales).

The phylogenetic relationships of Costaceae, a tropical monocotyledonous family sister to the gingers (Zingiberaceae), were investigated with a combination of two chloroplast loci (the trnL-F locus, including the trnL intron, the 3'trnL exon, and the trnL-F intergenic spacer, and the trnK locus, including the trnK intron and the matK coding region) and one nuclear locus (ITS1-5.8s-ITS2). The resulting parsimony analysis of selected taxa that demonstrate the range of floral morphological variation in the family shows that the Cadalvena-type [corrected] floral morphology is ancestral to the group and that both Tapeinochilos species and a Monocostus + Dimerocostus clade represent recent divergences. The genus Costus is broadly paraphyletic but Costus subgenus Eucostus K. Schum. represents a large monophyletic radiation that is poorly resolved. Within this clade, secondary analyses suggest that pollination syndrome, traditionally used for taxonomic and classification purposes within the genus Costus, is a relatively plastic trait of limited phylogenetic utility. This represents the first detailed investigation into intrageneric and interspecific evolutionary relationships within the family Costaceae and presents some novel evolutionary trends with respect to floral morphology and biogeography.

Chloroplasts↗
PubMed1992

The evolution of two west African populations.

The identification of genetically coherent populations is essential for understanding human evolution. Among the culturally uniform ethnic groups of west Africa, there are two geographically distinct populations with high frequencies of sickle-cell hemoglobin (HbS). Although the HbS mutation in each group is found on distinguishable chromosomes 11, these populations have been assumed to be parts of a single population. Analysis of mitochondrial DNA (mtDNA) in these populations demonstrated that the two populations identified by alternative chromosomes 11 bearing HbS have distinct distributions of mitochondrial genotypes, i.e., they are maternally separate. These studies also showed that, contrary to expectation, the mtDNA of some individuals is heteroplasmic. For nuclear loci, a comparison of the frequency of alternative alleles established that these populations are genetically distinct. Both the mitochondrial and nuclear data indicate that these populations have been separate for approximately 50,000 years. Although HbS in the two populations is usually attributed to recent, independent mutations, the duration of the separation and the observed geographic distribution of the population allow for the possibility of an ancient origin of HbS. Assuming an ancient mutation and considering the known biogeography, we suggest that HbS protected selected populations from malaria in rain forest refuges during the most recent ice age.

Africa, Western↗
PubMed1994

Chromosomal variation in the northwestern American newts of the genus Taricha (Caudata: Salamandridae).

Chromosomal variation was analysed in 22 populations of newts of the salmandrid genus Taricha of western North America, and compared with that of the eastern North American newts of the genus Notophthalmus. The karyotypes of the species Taricha and Notophthalmus were very similar. However, there was considerable variation in the distribution patterns of heterochromatins (revealed by C-banding) and in the sites of the nucleolar organizing region (NOR) (revealed by fluorochrome chromomycin A3 banding) within and between species of these two genera. Chromosomal variation patterns were interpreted in relation to a phylogenetic hypothesis derived from data on mitochondrial DNA sequences and allozyme variation. This study suggests that the pattern distributions of heterochromatins in chromosomes of Taricha are more derived than those of its sister taxon Notophthalmus. Furthermore, the chromosomal NOR types found in the southernmost and northernmost populations of T. granulosa, in the northernmost populations of T. t. sierrae, and in the southern populations of T. t. torosa are recently derived. The implications of this chromosomal variation for phylogeny and biogeography are discussed.

Animals↗
PubMed2004

Is the "Lost World" really lost? Palaeoecological insights into the origin of the peculiar flora of the Guayana Highlands.

The peculiar biogeography of the so-called "Lost World", i.e. the summits of sandstone tableaux ( tepuis) in the Neotropical Guyana region of Venezuela, has generated a debate regarding the factors that are thought to account for modern vegetation patterns in the region. Some argue that plant communities on these high-elevation summits reflect a long history of evolution in isolation, while others surmise that there has been substantial biotic interchange with the surrounding lowlands during glacial times. Until now, these apparently competing hypotheses have not been tested using palaeoecological methods. I used pollen analysis of Quaternary sediments and documented past vertical migrations of vegetation in response to climate changes, which supports the second hypothesis. Physiographical analysis, however, shows that about half the tableaux summits are too high for their flora to have reached the lowlands during the last glaciation, suggesting that a portion of the tableaux vegetation has always experienced some degree of biotic isolation. Thus, a component of the summit vegetation evolved in isolation, whereas other taxa experienced interchange, as reflected in endemism patterns among the tableaux summits. Biogeographical patterns on the summits are the result of complex evolutionary processes. The two hypotheses invoked to explain the vegetation patterns are not mutually exclusive, but instead complement one another.

Altitude↗
PubMed2005

Phylogeography of Australia's king brown snake (Pseudechis australis) reveals Pliocene divergence and Pleistocene dispersal of a top predator.

King brown snakes or mulga snakes (Pseudechis australis) are the largest and among the most dangerous and wide-ranging venomous snakes in Australia and New Guinea. They occur in diverse habitats, are important predators, and exhibit considerable morphological variation. We infer the relationships and historical biogeography of P. australis based on phylogenetic analysis of 1,249 base pairs from the mitochondrial cytochrome b, NADH dehydrogenase subunit 4 and three adjacent tRNA genes using Bayesian, maximum-likelihood, and maximum-parsimony methods. All methods reveal deep phylogenetic structure with four strongly supported clades comprising snakes from New Guinea (I), localities all over Australia (II), the Kimberleys of Western Australia (III), and north-central Australia (IV), suggesting a much more ancient radiation than previously believed. This conclusion is robust to different molecular clock estimations indicating divergence in Pliocene or Late Miocene, after landbridge dispersal to New Guinea had occurred. While members of clades I, III and IV are medium-sized, slender snakes, those of clade II attain large sizes and a robust build, rendering them top predators in their ecosystems. Genetic differentiation within clade II is low and haplotype distribution largely incongruent with geography or colour morphs, suggesting Pleistocene dispersal and recent ecomorph evolution. Significant haplotype diversity exists in clades III and IV, implying that clade IV comprises two species. Members of clade II are broadly sympatric with members of both northern Australian clades. Thus, our data support the recognition of at least five species from within P. australis (auct.) under various criteria. We discuss biogeographical, ecological and medical implications of our findings.

Animals↗
PubMed2001

Spatially realistic theory of metapopulation ecology.

Much of spatial ecology since the late 1960s has been dominated by two theories, the dynamic theory of island biogeography and the classical metapopulation theory. The latter theory largely replaced the former one in the 1980s, especially in conservation applications. It is only recently that ecologists have fully realized that a relatively simple general theory can be readily constructed that makes some of the simplifying assumptions of the two earlier theories unnecessary. The spatially realistic metapopulation theory thereby provides a more unified framework for spatial ecology than the island theory or the classical metapopulation theory. This article describes the application of the spatially realistic metapopulation theory to real metapopulations living in highly fragmented landscapes. I discuss the principal messages for population ecology and conservation biology, and I also place this theory into a broader context of other approaches to spatial ecology.

Animals↗
PubMed2003

Cross-species amplification of mitochondrial DNA sequence-tagged-site markers in conifers: the nature of polymorphism and variation within and among species in Picea.

Primers previously developed to amplify specific non-coding regions of the mitochondrial genome in Angiosperms, and new primers for additional non-coding mtDNA regions, were tested for their ability to direct DNA amplification in 12 conifer taxa and to detect sequence-tagged-site (STS) polymorphisms within and among eight species in Picea. Out of 12 primer pairs, nine were successful at amplifying mtDNA in most of the taxa surveyed. In conifers, indels and substitutions were observed for several loci, allowing them to distinguish between families, genera and, in some cases, between species within genera. In Picea, interspecific polymorphism was detected for four loci, while intraspecific variation was observed for three of the mtDNA regions studied. One of these (SSU rRNA V1 region) exhibited indel polymorphisms, and the two others ( nad1 intron b/c and nad5 intron1) revealed restriction differences after digestion with Sau3AI (PCR-RFLP). A fourth locus, the nad4L- orf25 intergenic region, showed a multibanding pattern for most of the spruce species, suggesting a possible gene duplication. Maternal inheritance, expected for mtDNA in conifers, was observed for all polymorphic markers except the intergenic region nad4L- orf25. Pooling of the variation observed with the remaining three markers resulted in two to six different mtDNA haplotypes within the different species of Picea. Evidence for intra-genomic recombination was observed in at least two taxa. Thus, these mitotypes are likely to be more informative than single-locus haplotypes. They should be particularly useful for the study of biogeography and the dynamics of hybrid zones.

Base Sequence↗