Cryptic vicariance in Gulf of California fishes parallels vicariant patterns found in Baja, California mammals and reptiles

Comparisons across multiple taxa can often clarify the histories of biogeographic regions. In particular, historic barriers to movement should affect multiple species and, thus, result in a pattern of concordant intraspecific genetic divisions among species. A striking example of such comparative phylogeography is the recent observation that populations of many small mammals and reptiles living on the Baja, California peninsula have a large genetic break between northern and southern peninsular populations. In the present study, I demonstrate that five species of near-shore fishes living on the Baja coastline of the Gulf of California share this genetic pattern. The simplest explanation for this concordant genetic division within both terrestrial and marine vertebrates is that the Baja peninsula was fragmented by a Plio-Pleistocene marine seaway and that this seaway posed a substantial barrier to movement for near-shore fishes. The genetic divisions within Gulf of California fishes also coincide with recognized biogeographic regions based on fish community composition and several environmental factors. It is likely that adaptation to regional environments and present-day oceanographic circulation limits gene exchange between biogeographic regions and helps maintain evidence of past vicariance.

Differential patterns of Male and Female mtDNA exchange across the Atlantic Ocean in the blue mussel, Mytilus edulis

Comparisons among loci with differing modes of inheritance can reveal unexpected aspects of population history. We employ a multilocus approach to ask whether two types of independently assorting mitochondrial DNAs (maternally and paternally inherited: F- and M-mtDNA) and a nuclear locus (ITS) yield concordant estimates of gene flow and population divergence. The blue mussel, Mytilus edulis, is distributed on both North American and European coastlines and these populations are separated by the waters of the Atlantic Ocean. Gene flow across the Atlantic Ocean differs among loci, with F-mtDNA and ITS showing an imprint of some genetic interchange and M-mtDNA showing no evidence for gene flow. Gene flow of F-mtDNA and ITS causes trans-Atlantic population divergence times to be greatly underestimated for these loci, although a single trans-Atlantic population divergence time (1.2 MYA) can be accommodated by considering all three loci in combination in a coalescent framework. The apparent lack of gene flow for M-mtDNA is not readily explained by different dispersal capacities of male and female mussels. A genetic barrier to M-mtDNA exchange between North American and European mussel populations is likely to explain the observed pattern, perhaps associated with the double uniparental system of mitochondrial DNA inheritance.

Positive selection on an acrosomal sperm protein, M7 lysin, in three species of the mussel genus Mytilus

Marine invertebrate sperm proteins are particularly interesting because they are characterized by positive selection and are likely to be involved in prezyogotic isolation and, thus, speciation. Here, we present the first survey of inter and intraspecific variation of a bivalve sperm protein among a group of species that regularly hybridize in nature. M7 lysin is found in sperm acrosomes of mussels and dissolves the egg vitelline coat, permitting fertilization. We sequenced multiple alleles of the mature protein-coding region of M7 lysin from allopatric populations of mussels in the Mytilus edulis species group (M. edulis, M. galloprovincialis, and M. trossulus). A significant McDonald-Kreitman test showed an excess of fixed amino acid replacing substitutions between species, consistent with positive selection. In addition, Kolmogorov-Smirnov tests showed significant heterogeneity in polymorphism to divergence ratios for both synonymous variation and combined synonymous and non-synonymous variation within M. galloprovincialis. These results indicate that there has been adaptive evolution at M7 lysin and, furthermore, shows that positive selection on sperm proteins can occur even when post-zygotic reproductive isolation is incomplete.

When oceans meet: a teleost shows secondary intergradation at an Indian-Pacific interface

The Indo-West Pacific is characterized by extraordinary marine species diversity. The evolutionary mechanisms responsible for generating this diversity remain puzzling, but are often linked to Pleistocene sea level fluctuations. The impact of these sea level changes on the population genetic architecture of the estuarine fish Lates calcarifer are investigated via a natural experiment in a region of the Indo-West Pacific known to have undergone considerable change during the Pleistocene. L. calcarifer, a coastline-restricted catadromous teleost, provides an excellent model for studying the effects of sea level change as its habitat requirements potentially make it sensitive to the region's physical history. Evidence was found for a large phylogenetic break (4% mtDNA control region; 0.47% ATPase 6 and 8) either side of the Torres Strait, which separates the Western Pacific and Indian Oceans, although some mixing of the clades was evident. This suggests clinal secondary introgression of the clades via contemporary gene flow. Further, populations on Australia's east coast appear to have passed through a bottleneck. This was linked to the historical drying of the Great Barrier Reef coastal lagoon, which resulted in a significant loss of habitat and forced retreat into isolated refugia. These results suggest that historical eustatic changes have left a significant imprint on the molecular diversity within marine species as well as among them in the Indo-West Pacific.

A global marker database for Phytophthora infestans

A marker database was compiled for isolates of the potato and tomato late blight pathogen, Phytophthora infestans, originating from 41 locations which include 31 countries plus 10 regions within Mexico. Presently, the database contains information on 1,776 isolates for one or more of the following markers: restriction fragment length polymorphism (RFLP) fingerprint consisting of 23 bands; mating type; dilocus allozyme genotype; mitochondrial DNA haplotype; sensitivity to the fungicide metalaxyl; and virulence. In the database, 305 entries have unique RFLP fingerprints and 258 entries have unique multilocus genotypes based on RFLP fingerprint, dilocus allozyme genotype, and mating type. A nomenclature is described for naming multilocus genotypes based on the International Organization for Standardization (ISO) two-letter country code and a unique number, Forty-two previously published multilocus genotypes are represented in the database with references to publications. As a result of compilation of the database, seven new genotypes were identified and named. Cluster analysis of genotypes from clonally propagated populations worldwide generally confirmed a previously published classification of old and new genotypes. Genotypes from geographically distant countries were frequently clustered, and several old and new genotypes were found in two or more distant countries. The cluster analysis also demonstrated that A2 genotypes from Argentina differed from all others. The database is available via the Internet, and thus can serve as a resource for Phytophthora workers worldwide.

Strong genetic structuring in a habitat specialist, the Oxleyan Pygmy Perch Nannoperca oxleyana

This study used allozyme and mitochondrial DNA variation to examine genetic structure in the Oxleyan Pygmy Perch Nannoperca oxleyana. This small-bodied freshwater fish has a very restricted distribution occurring only in some small coastal streams in south-east Queensland and northern New South Wales. It was expected that subpopulations may contain little genetic variation and be highly differentiated from one another. The results, based on allozyme and mitochondrial DNA control region variation were in agreement with these expectations. Allozyme variation was very low overall, with only one locus showing variation at most sites. The high differentiation was because a different locus tended to be polymorphic at each site. Mitochondrial variation within sites was also low, but some sites had unique haplotypes. The patterns of similarity among mitochondrial DNA haplotypes were not as expected from geographical proximity alone. In particular, although some northern sites had unique haplotypes, four sites spread along 200 km of coastline were remarkably similar, sharing the same common haplotype at similar frequencies. We suggest that these four streams may have had a confluence relatively recently, possibly when sea levels were lower, 8000-10 000 BP.

Genetic population structure of the catadromous perciform: Macquaria novemaculeata (Percichthyidae)

Genetic population structure in the catadromous Australian bass Macquaria novemaculeata was investigated using samples from four locations spanning 600 km along the eastern Australian coastline. Both allozymes and mtDNA control region sequences were examined. Population subdivision estimates based on allozymes revealed low levels of population structuring (G(st)=0.043, P<0.05). However, mtDNA indicated moderate levels of geographic population structure (G(st)=0.146, P<0.01). Phylogenetic analysis of mtDNA control region sequences (mean sequence divergence 1.9%) indicated little phylogeographic structuring. Results suggested that genotypic variation within each river population, while bring affected primarily by genetic drift, was also prevented from more significant divergence by homogenizing levels of gene flow-synonymous with a one-dimensional stepping-stone model of population structure. The catadromous life history of Macquaria novemaculeata was considered to br influential on the pattern of population structure displayed. Results were compared to the few population genetic studies involving catadromous fishes, indicating that catadromy alone is unlikely to be a good predictor of population structure. A more comprehensive suite of biological characteristics than simple life-history traits must be considered fully to allow reliable predictive models of population structure to be formulated. (C) 1997 The Fisheries Society of the British Isles.

A total-evidence phylogeny of ticks provides insights into the evolution of life cycles and biogeography

We inferred the phylogeny of 33 species of ticks from the subfamilies Rhipicephalinae and Hyalomminae from analyses of nuclear and mitochondrial DNA and morphology. We used nucleotide sequences from 12S rRNA, cytochrome c oxidase I, internal transcribed spacer 2 of the nuclear rRNA, and 18S rRNA. Nucleotide sequences and morphology were analyzed separately and together in a total-evidence analysis. Analyses of the five partitions together (3303 characters) gave the best-resolved and the best-supported hypothesis so far for the phylogeny of ticks in the Rhipicephalinae and Hyalomminae, despite the fact that some partitions did not have data for some taxa. However, most of the hidden conflict (lower support in the total-evidence analyses compared to that in the individual analyses) was found in those partitions that had taxa without data. The partitions with complete taxonomic sampling had more hidden support (higher support in the total-evidence analyses compared to that in the separate-partition analyses) than hidden conflict. Mapping of geographic origins of ticks onto our phylogeny indicates an African origin for the Rhipicephalinae sensu lato (i.e., including Hyalomma spp.), the Rhipicephalus-Boophilus lineage, the Dermacentor-Anocentor lineage, and the Rhipicephalus-Booophilus-Nosomma-Hyalomma-Rhipicentor lineage. The Nosomma-Hyalomma lineage appears to have evolved in Asia. Our total-evidence phylogeny indicates that (i) the genus Rhipicephalus is paraphyletic with respect to the genus Boophilus, (ii) the genus Dermacentor is paraphyletic with respect to the genus Anocentor, and (iii) some subgenera of the genera Hyalomma and Rhipicephalus are paraphyletic with respect to other subgenera in these genera. Study of the Rhipicephalinae and Hyalomminae over the last 7 years has shown that analyses of individual datasets (e.g., one gene or morphology) seldom resolve many phylogenetic relationships, but analyses of more than one dataset can generate well-resolved phylogenies for these ticks. (C) 2001 Academic Press.

Comparative phylogeography of two open forest frogs from eastern Australia

We investigated the phylogeography of two closely related Australian frog species from open forest habitats, Limnodynastes tasmaniensis and L. peronii, using mitochondrial ND4 sequence data. Comparison of our results with previous work on Litoria fallax allowed us to test the generality of phylogeographic patterns among non-rainforest anurans along the east coast of Australia. In general, there was no strong evidence for congruence between overall patterns of genetic structure in the three species. However, phylogenetic breaks congruent with the position of the Burdekin Gap were detected at some level in all species. As previously noted for closed forest taxa, this area of dry habitat appears to have been an important influence on the evolution of several open forest taxa. There were broad geographic similarities in the phylogenetic structuring of southern populations of L. peronii and L. tasmaniensis. Contrarily, although the McPherson Range has previously been noted to coincide geographically with a major mtDNA phylogenetic break in Litoria fallax this pattern is not apparent in L. peronii or L. tasmaniensis. It appears that major phylogeographic splits within L. peronii and L. tasmaniensis may predate the Quaternary. We conclude that phylogeographies of open forest frogs are complex and more difficult to predict than for rainforest taxa, mainly due to an absence of palaeomodels for historical distributions of non-rainforest habitats. (C) 2001 The Linnean Society of London.

Resolution of natural groups using iterative assignment tests: an example from two species of Australian native rats (Rattus)

Sympatric individuals of Rattus fuscipes and Rattus leucopus, two Australian native rats from the tropical wet forests of north Queensland, are difficult to distinguish morphologically and are often confused in the field. When we started a study on fine-scale movements of these species, using microsatellite markers, we found that the species as identified in the field did not form coherent genetic groups. In this study, we examined the potential of an iterative process of genetic assignment to separate specimens from distinct (e.g. species, populations) natural groups. Five loci with extensive overlap in allele distributions between species were used for the iterative process. Samples were randomly distributed into two starting groups of equal size and then subjected to the test. At each iteration, misassigned samples switched groups, and the output groups from a given round of assignment formed the input groups for the next round. All samples were assigned correctly on the 10th iteration, in which two genetic groups were clearly separated. Mitochondrial DNA sequences were obtained from samples from each genetic group identified by assignment, together with those of museum voucher specimens, to assess which species corresponded to which genetic group. The iterative procedure was also used to resolve groups within species, adequately separating the genetically identified R. leucopus from our two sampling sites. These results show that the iterative assignment process can correctly differentiate samples into their appropriate natural groups when diagnostic genetic markers are not available, which allowed us to resolve accurately the two R. leucopus and R. fuscipes species. Our approach provides an analytical tool that may be applicable to a broad variety of situations where genetic groups need to be resolved.

The life-history basis of latitudinal diversity gradients: how do species traits vary from the poles to the equator.

1. Latitudinal variation among species in life-history traits is often suggested to contribute to high tropical species richness. However, traditional methods of analysing such variation rarely control for phylogeny and latitudinal range overlap between species, potentially giving misleading results. 2. Using a method of pairwise independent contrasts which overcomes these problems, I tested for latitudinal variation among bird species in a number of traits which have been linked, theoretically or empirically, with both latitude and species richness. 3. This method indicates strong support for Rapoport's Rule and decreasing clutch size towards the equator in both hemispheres, but only partial support for decreasing body size and ecological generalism towards the equator. 4. Indirect measures of sexual selection (sexual dichromatism and size dimorphism) show no variation with latitude; an apparent increase in dichromatism towards the equator is shown to be an artefact of phylogeny. 5. Many of the associations between life history and latitude were not detected by traditional cross-species analyses, highlighting the importance of incorporating phylogeny and overlap in studies of geographical life-history variation. Establishing associations between life-history traits and latitude does not prove, but is a necessary prerequisite for., a link between these traits and latitudinal diversity gradients.

Molecular clocks in reptiles: Life history influences rate of molecular evolution

Life history has been implicated as a determinant of variation in rate of molecular evolution amongst vertebrate species because of a negative correlation between bode size and substitution rate for many Molecular data sets. Both the generality and the cause of the negative bode size trend have been debated, and the validity of key studies has been questioned (particularly concerning the failure to account for phylogenetic bias). In this study, a comparative method has been used to test for an association between a range of life-history variables-such as body size age at maturity, and clutch size-and DNA substitution rate for three genes (NADH4, cytochrome b, and c-mos). A negative relationship between body size and rate of molecular evolution was found for phylogenetically independent pairs of reptile species spanning turtles. lizards. snakes, crocodile, and tuatara. Although this Study was limited by the number of comparisons for which both sequence and lite-history data were available, the results, suggest that a negative bode size trend in rate of molecular evloution may be a general feature of reptile molecular evolution. consistent with similar studies of mammals and birds. This observation has important implications for uncovering the mechanisms of molecular evolution and warns against assuming that related lineages will share the same substitution rate (a local molecular clock) in order to date evolutionary divergences from DNA sequences.

Reconciling paleodistribution models and comparative phylogeography in the Wet Tropics rainforest land snail Gnarosophia bellendenkerensis (Brazier 1875)

Comparative phylogeography has proved useful for investigating biological responses to past climate change and is strongest when combined with extrinsic hypotheses derived from the fossil record or geology. However, the rarity of species with sufficient, spatially explicit fossil evidence restricts the application of this method. Here, we develop an alternative approach in which spatial models of predicted species distributions under serial paleoclimates are compared with a molecular phylogeography, in this case for a snail endemic to the rainforests of North Queensland, Australia. We also compare the phylogeography of the snail to those from several endemic vertebrates and use consilience across all of these approaches to enhance biogeographical inference for this rainforest fauna. The snail mtDNA phylogeography is consistent with predictions from paleoclimate modeling in relation to the location and size of climatic refugia through the late Pleistocene-Holocene and broad patterns of extinction and recolonization. There is general agreement between quantitative estimates of population expansion from sequence data (using likelihood and coalescent methods) vs. distributional modeling. The snail phylogeography represents a composite of both common and idiosyncratic patterns seen among vertebrates, reflecting the geographically finer scale of persistence and subdivision in the snail. In general, this multifaceted approach, combining spatially explicit paleoclimatological models and comparative phylogeography, provides a powerful approach to locating historical refugia and understanding species' responses to them.

A molecular phylogeny of rainbow skinks (Scincidae : Carlia): taxonomic and biogeographic implications

The phylogenetic relationships amongst 29 species of Carlia and Lygisaurus were estimated using a 726-base-pair segment of the protein-coding mitochondrial ND4 gene. Results do not support the recent resurrection of the genus Lygisaurus. Although most Lygisaurus species formed a single clade, this clade is nested within Carlia and includes Carlia parrhasius. Due to this new molecular evidence, and the paucity of diagnostic morphological characters separating the genera, Lygisaurus de Vis 1884 is re-synonymised with Carlia Gray 1845. Our analysis is also inconsistent with a previous suggestion that Lygisaurus timlowi should be removed to Menetia, a genus that is distantly related relative to outgroups used here. Intraspecific variation in Carlia is, in several instances, greater than interspecific distance. The most strikingly divergent lineages are found within C. rubrigularis, which appears to be paraphyletic, with southern populations more closely related to C. rhomboidalis than to northern populations of C. rubrigularis. The two C. rubrigularis-C. rhomboidalis lineages form part of a major polytomy at an intermediate level of divergence. Lack of resolution at this level, however, does not appear to be due to saturation or loss of phylogenetic signal. Rather, the polytomy probably reflects a period of relatively rapid diversification that occurred sometime during the Miocene.