EVOLUTIONARY INFERENCES FROM RESTRICTION MAPS OF MITOCHONDRIAL DNA FROM NINE TAXA OF XENOPUS FROGS

GEOGRAPHIC DISTRIBUTION OF MITOCHONDRIAL DNA VARIANTS AND THE HISTORICAL BIOGEOGRAPHY OF THE SPOTTED SALAMANDER, AMBYSTOMA MACULATUM

I analyzed geographic partitioning of mitochondrial DNA (mtDNA) restriction-site variants in the spotted salamander, Ambystoma maculatum. Two highly divergent and geographically separate genetic lineages were identified that differed by a minimum of 19 restriction sites (6% sequence divergence). One of the lineages has a disjunct distribution with very closely related haplotypes occurring in Missouri, Arkansas, North Carolina, and Virginia. The other lineage is found in Michigan, Illinois, and Alabama. The geographic separation of highly divergent mtDNA haplotypes, a pattern that was predicted based on the sedentary nature of these salamanders, is evidence for long-term barriers to gene flow. In contrast, the large-scale disjunction of very similar haplotypes suggests recent, long-distance gene flow and does not match the phylogeographic expectation for a small terrestrial vertebrate. I explain this potential contradiction in the level of importance assigned to gene flow by a scenario in which historical barriers to gene flow account for the two divergent mtDNA assemblages, but stochastic sorting of ancestral polymorphism is responsible for the large-scale geographic disjunction. Ten of 16 populations collected in the Ozark Highlands were fixed for the same haplotype. I attribute this lack of detectable variation to recent colonization of this area, a hypothesis that is supported by paleoecological data and demonstrates the potential benefits of combining data from paleobotany, geology, and other disciplines to reconstruct the historical biogeography of a species.

EVOLUTIONARY ASSOCIATIONS OF BROOD PARASITIC FINCHES (VIDUA) AND THEIR HOST SPECIES: ANALYSES OF MITOCHONDRIAL DNA RESTRICTION SITES

The species-specific associations of the African brood parasitic finches Vidua with their estrildid finch host species may have originated by cospeciation with the host species or by later colonizations of new hosts. Predictions of these alternative models were tested in two species groups of brood parasites (indigobirds, paradise whydahs) and their hosts. Phylogenetic analyses suggested that the brood parasites and their hosts did not speciate in parallel. The parasitic indigobirds share mitochondrial haplotypes with each other, and species limits in both indigobirds and paradise whydahs do not correspond with their gene trees. Different parasite species within a region are more closely related to each other than any is to parasites that are associated with its same host species in other regions of Africa. There is little genetic difference between parasite species D̂_i,j < 0.001 in the indigobirds, D̂_i,j = 0.01 in the whydahs). Genetic distances D̂_i,j between the parasite species are less than the genetic distances between their corresponding host species in all parasite-host comparisons, and average only 7.2% as large in the indigobirds as in their hosts and 42% as large in the paradise whydahs as in their hosts. A phylogenetic model that allows ancestral haplotype polymorphisms to be retained in descendant species was compared to a constraint model of species monophyly requiring all but the one ancestral haplotype to be independently derived within each species. The constraint model increases the length of the indigobird tree by 50% over that of the model of retained ancestral polymorphisms; the difference is statistically significant. Both phylogenetic and distance analyses indicate that the brood parasites have become associated with their host species through host switches and independent colonizations of the hosts, rather than through parallel cospeciation with them. The molecular genetic results are supported by recent discoveries of additional host species that are associated with the indigobirds in the field and by variation in the species-specific song behaviors of the brood parasites.

HALDANE'S RULE AND SEX BIASSED GENE FLOW BETWEEN TWO HYBRIDIZING FLYCATCHER SPECIES (FICEDULA ALBICOLLIS AND F. HYPOLEUCA, AVES: MUSCICAPIDAE)

The collared flycatcher (Ficedula albicollis) and the pied flycatcher (F. hypoleuca) hybridize where their geographic ranges overlap. Restriction fragment comparison of 5% of the mitochondrial genome showed a sequence divergence of 10% between these flycatcher species. This degree of sequence divergence between a closely related pair of bird species is unusually high and contrasts with the low level of divergence between F. albicollis and F. hypoleuca in nuclear genes (Nei's D = 0.0006) revealed by enzyme electrophoresis. The low nuclear differentiation is explained by sex biassed gene flow and introgression in nuclear genes (via fertile male hybrids), while the high mitochondrial DNA sequence divergence is preserved by sterility of female hybrids, which prevents mitochondrial introgression. This pattern is in accordance with Haldane's rule and is supported by field data on hybrid fertility. The high mtDNA differentiation could be explained by transfer of mitochondrial DNA from a third species during a past period of hybridization.

SPECIATION BY POLYPLOIDY IN TREEFROGS: MULTIPLE ORIGINS OF THE TETRAPLOID, HYLA VERSICOLOR

Speciation by polyploidy is rare in animals, yet, in vertebrates, there is a disproportionate concentration of polyploid species in anuran amphibians. Sequences from the cytochrome b gene of the mitochondrial DNA (mtDNA) were used to determine phylogenetic relationships among 37 populations of the diploid-tetraploid species pair of gray treefrogs, Hyla chrysoscelis and Hyla versicolor. The diploid species, H. chrysoscelis, consists of an eastern and a western lineage that have 2.3% sequence divergence between them. The tetraploid species, H. versicolor, had at least three separate, independent origins. Two of the tetraploid lineages are more closely related to one or the other of the diploid lineages (0.18%-1.4% sequence divergence) than they are to each other (1.9%-3.4% sequence divergence). The maternal ancestor of the third tetraploid lineage is unknown. The phylogenetic relationships between the two species and among lineages within each species support the hypothesis of multiple origins of the tetraploid lineages.

ADAPTIVE RADIATION OF DAY-GECKOS (PHELSUMA) IN THE SEYCHELLES ARCHIPELAGO: A PHYLOGENETIC ANALYSIS

A phylogenetic analysis using characters derived from mitochondrial DNA was used to show that the species of Phelsuma in the Seychelles Islands represent a single, monophyletic lineage that has diversified as a result of both historical and ecological factors. In the distant past, the Seychelles archipelago was physically invaded by a single species of Phesluma. Separate eustatic sea level changes likely led first to allopatric speciation and then to the secondary contact of these sister species. Differences in the relative timing of the secondary contact between island groups resulted in P. sundbergi evolving an intermediate body size in the group of islands associated with Mahé and a large body size, while sympatric with P. astriata, in the group of islands associated with Praslin. Ecological information was used to support the conclusion that the actual evolutionary mechanism for the body size shift was a response to frequency dependent natural selection of P. sundbergi in single-species and two-species competitive regimes.

Description of a new octoploid frog species (Anura: Pipidae: Xenopus) from the Democratic Republic of the Congo, with a discussion of the biogeography of African clawed frogs in the Albertine Rift

We describe a new octoploid species of African clawed frog (Xenopus) from the Lendu Plateau in the northern Albertine Rift of eastern Democratic Republic of the Congo. This species is the sister taxon of Xenopus vestitus (another octoploid), but is distinguished by a unique morphology, vocalization and molecular divergence in mitochondrial and autosomal DNA. Using a comprehensive genetic sample, we provide new information on the species ranges and intra-specific diversity of African clawed frogs from the Albertine Rift, including the details of a small range extension for the critically endangered Xenopus itombwensis and previously uncharacterized variation in Xenopus laevis. We also detail a new method for generating cytogenetic preparations in the field that can be stored at room temperature for up to 3 weeks. While extending our understanding of the extant diversity in the Albertine Rift, this new species highlights components of species diversity in ancestral African clawed frogs that are not represented by known extant descendants.

Experimental analysis of lens-forming capacity in Xenopus borealis larvae

Previously, the only anuran amphibians known to have the capacity to regenerate a lens after lentectomy were Xenopus laevis and Xenopus tropicalis. This regeneration process occurs during the larval life through transdifferentiation of the outer cornea promoted by inductive factors produced by the retina and accumulated inside the vitreous chamber. However, the capacity of X. tropicalis to regenerate a lens is much lower than that of X. laevis. This study demonstrates that Xenopus borealis, a species more closely related to X. laevis than to X. tropicalis, is not able to regenerate a lens after lentectomy. Nevertheless, some morphological modifications corresponding to the first stages of lens regeneration in X. laevis were observed in the outer cornea of X. borealis. This suggested that in X borealis the regeneration process was blocked at early stages. Results from histological analysis of X. borealis and X. laevis lentectomized eyes and from implantation of outer cornea fragments into the vitreous and anterior chambers demonstrated that: (i) in X. borealis eye, the lens-forming competence in the outer cornea and inductive factors in the vitreous chamber are both present, (ii) no inhibiting factors are present in the anterior chamber, the environment where lens regeneration begins, (iii) the inability of X. borealis to regenerate a lens after lentectomy is due to an inhibiting action exerted by the inner cornea on the spreading of the retinal factor from the vitreous chamber towards the outer cornea. This mechanical inhibition is assured by two distinctive features of X. borealis eye in comparison with X. laevis eye: (i) a weaker and slower response to the retinal inducer by the outer cornea; (ii) a stronger and faster healing of the inner cornea. Unlike X. tropicalis and similar to X. laevis, in X. borealis the competence to respond to the retinal factor is not restricted to the corneal epithelium but also extends to the pericorneal epidermis.

Mitochondrial DNA differentiation in the Japanese brown frog Rana japonica as revealed by restriction endonuclease analysis

To elucidate mtDNA differentiation in the Japanese brown frog Rana japonica, and compare it with results from allozyme analysis and crossing experiments, RFLP analysis was conducted on 78 frogs from 16 populations in Honshu. Purified mtDNA was digested with eight six-base recognizing restriction enzymes and analyzed by 1% agarose-slab gel electrophoresis. Cleavage patterns of the mtDNA showed three distinct genome size classes: small (18.5 kb), middle (20.0 kb) and large (21.5 kb). Ten haplotypes (I approximately X) were observed among the 16 populations. The expected nucleotide divergences within populations ranged from 0 to 0.47% with a mean of 0.08%. The net nucleotide divergences among 16 populations ranged from 0 to 7.74% with a mean of 3.49%. The UPGMA dendrogram and NJ tree, which were constructed based on the net nucleotide divergences, showed that R. japonica diverged first into the eastern and western groups. The eastern group subsequently differentiated into a subgroup containing six populations and the Akita population, and the western group divided into several subgroups. These results, as well as the results of allozyme analysis and crossing experiments, suggest the the eastern and western groups have experienced secondary contact, and introgression has occurred in the Akita population.

Phylogenetic evidence for horizontal transfer of an intervening sequence between species in a spirochete genus

The 23S rRNA genes (rrl genes) of some strains of certain species of the spirochete genus Leptospira carry an intervening sequence (IVS) of 485 to 759 bases flanked by terminal inverted repeat and encoding an open reading frame for a putative protein of over 120 amino acids. The structure and the sporadic distribution of the IVS suggest that it might be a mobile element that can be horizontally transferred within or between species. Phylogenetic hypotheses based on the sequences for six IVS open reading frames from various species were compared with hypotheses constructed by using DNA sequences from the 16S rRNA gene (rrs), which is not closely linked to rrl in this genus. The predicted phylogenies for the IVS and rrs differed in a major respect: one strain that claded with L. weillii in the tree based on the rrs data claded with L. noguchi in the tree based on the IVS data. Neither set of data supported a tree in which this strain was constrained to be in the same clade as was supported by the other set of data. This result indicates a probable horizontal transfer of the IVS from a recent ancestor of L. noguchi to a recent ancestor of one of the L. weillii strains. This observation is the first indication of horizontal transfer of elements encoded on the chromosomes of spirochetes.

Leptospira species categorized by arbitrarily primed polymerase chain reaction (PCR) and by mapped restriction polymorphisms in PCR-amplified rRNA genes

Reference strains from 48 selected serovars representing eight species of Leptospira were examined by two polymerase chain reaction (PCR)-based strategies. First, mapped restriction site polymorphisms (MRSP) were examined in PCR products from portions of rrs (16S rRNA gene) and rrl (23S rRNA gene). Twenty MRSP and 2 length polymorphisms were used to group reference strains into 16 MRSP profiles. Species assignments were consistent with those obtained by a second method, genomic fingerprinting with arbitrarily primed PCR, in which strains within a species were characterized by many shared arbitrarily primed PCR products. The results of both of these methods were in general agreement with those of previous studies that used DNA-DNA relatedness and confirmed the high level of divergence among the recognized species of Leptospira. However, Leptospira meyeri serovar ranarum and evansi strains were indistinguishable from some strains of Leptospira interrogans sensu stricto. Intervening sequences of about 485 to 740 bp were located near base 1230 in rrl of some strains.