Potential host range expansion of the retroviruses.
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Population-level history of the wrentit (Chamaea fasciata): implications for comparative phylogeography in the California Floristic Province.
The phylogeography of a variety of species has been studied within the California Floristic Province; however, few studies have examined genetic variation in bird species across the entire region. This study uses mitochondrial DNA data to investigate the phylogeography of the wrentit (Chamaea fasciata), a sedentary bird native to scrub and chaparral habitats of this region. Analysis of molecular variance shows geographic structure, and maximum likelihood, Bayesian, and parsimony analyses consistently identify six main clades that are each restricted geographically. Nested clade phylogeographic analyses infer an overall range expansion for the entire cladogram, and a range expansion is also inferred from the mismatch distribution. Thus, our results suggest that the wrentit was isolated into southern refugia during the Pleistocene and has undergone a recent range expansion. Southern refugia and a range expansion were also identified in a previous study of the California thrasher (Toxostoma redivivum). The wrentit did not show marked divergence between northern and southern California defined by the Transverse Ranges, a pattern seen in a variety of other taxa within this region, including some birds.
Animals↗
Diluting the founder effect: cryptic invasions expand a marine invader's range.
Most invasion histories include an estimated arrival time, followed by range expansion. Yet, such linear progression may not tell the entire story. The European green crab (Carcinus maenas) was first recorded in the US in 1817, followed by an episodic expansion of range to the north. Its population has recently exploded in the Canadian Maritimes. Although it has been suggested that this northern expansion is the result of warming sea temperatures or cold-water adaptation, Canadian populations have higher genetic diversity than southern populations, indicating that multiple introductions have occurred in the Maritimes since the 1980s. These new genetic lineages, probably from the northern end of the green crab's native range in Europe, persist in areas that were once thought to be too cold for the original southern invasion front. It is well established that ballast water can contain a wide array of nonindigenous species. Ballast discharge can also deliver genetic variation on a level comparable to that of native populations. Such gene flow not only increases the likelihood of persistence of invasive species, but it can also rapidly expand the range of long-established nonindigenous species.
Animals↗
Phylogeography of Biomphalaria glabrata and B. pfeifferi, important intermediate hosts of Schistosoma mansoni in the New and Old World tropics.
The historical phylogeography of the two most important intermediate host species of the human blood fluke Schistosoma mansoni, B. glabrata in the New World, and B. pfeifferi in the Old World, was investigated using partial 16S and ND1 sequences from the mitochondrial genome. Nuclear sequences of an actin intron and internal transcribed spacer (ITS)-1 were also obtained, but they were uninformative for the relationships among populations. Phylogenetic analyses based on mtDNA revealed six well-differentiated clades within B. glabrata: the Greater Antilles, Venezuela and the Lesser Antilles, and four geographically overlapping Brazilian clades. Application of a Biomphalaria-specific mutation rate gives an estimate of the early Pleistocene for their divergence. The Brazilian clades were inferred to be the result of fragmentation, due possibly to climate oscillations, with subsequent range expansion producing the overlapping ranges. Within the Venezuela and Lesser Antilles clade, lineages from each of these areas were estimated to have separated approximately 740 000 years ago. Compared to B. glabrata, mitochondrial sequences of B. pfeifferi are about 4x lower in diversity, reflecting a much younger age for the species, with the most recent common ancestor of all haplotypes estimated to have existed 880 000 years ago. The oldest B. pfeifferi haplotypes occurred in southern Africa, suggesting it may have been a refugium during dry periods. A recent range expansion was inferred for eastern Africa less than 100 000 years ago. Several putative species and subspecies, B. arabica, B. gaudi, B. rhodesiensis and B. stanleyi, are shown to be undifferentiated from other B. pfeifferi populations.
Africa↗
Out of Africa and back again: nested cladistic analysis of human Y chromosome variation.
We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544 individuals from Africa, Asia, Europe, Oceania, and the New World. Phylogenetic analyses of these nine sites resulted in a tree for 10 distinct Y haplotypes with a coalescence time of approximately 150,000 years. The 10 haplotypes were unevenly distributed among human populations: 5 were restricted to a particular continent, 2 were shared between Africa and Europe, 1 was present only in the Old World, and 2 were found in all geographic regions surveyed. The ancestral haplotype was limited to African populations. Random permutation procedures revealed statistically significant patterns of geographical structuring of this paternal genetic variation. The results of a nested cladistic analysis indicated that these geographical associations arose through a combination of processes, including restricted, recurrent gene flow (isolation by distance) and range expansions. We inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model. A second and more recent range expansion brought Asian Y chromosomes back to Africa without replacing the indigenous African male gene pool. Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements. Finally, a comparison of our results with those from nested cladistic analyses of human mtDNA and beta-globin data revealed different patterns of inferences for males and females concerning the relative roles of population history (range expansions) and population structure (recurrent gene flow), thereby adding a new sex-specific component to models of human evolution.
Africa↗
Modeling biological invasions into periodically fragmented environments.
Range expansion of a single species in a regularly striped environment is studied by using an extended Fisher model, in which the rates of diffusion and reproduction periodically fluctuate between favorable and unfavorable habitats. The model is analyzed for two initial conditions: the initial population density is concentrated on a straight line or at the origin. For each case, we derive a mathematical formula which characterizes the spatio-temporal pattern of range expansion. When initial distribution starts from a straight line, it evolves to a traveling periodic wave (TPW), whose frontal speed is analytically determinable. When the range starts from the origin, it tends to expand radially at a constant average speed in each direction (ray speed) keeping its frontal envelope in a similar shape. By examining the relation between the ray speed and the TPW speed, we derive the ray speed in a parametric form, from which the envelope of the expanding range can be predicted. Thus we analyze how the pattern and speed of the range expansion are affected by the pattern and scale of fragmentation, and the qualities of favorable and unfavorable habitats. The major results include: (1). The envelope of the expanding range show a variety of patterns, nearly circular, oval-like, spindle-like, depending on parameter values; (2). All these patterns are elongated in the direction of stripes; (3). When the scale of fragmentation is enlarged without changing the relative spatial pattern, the ray speed in any direction increases, i.e., the rate of range expansion increases.
Algorithms↗
Seed and pollen flow in expanding a species' range.
The distinct processes of gene flow via seeds and pollen in hermaphrodite plants provide a biological basis for interpreting their different roles in expanding a species' range. A species' range is primarily expanded through the colonization process by seed dispersal and followed by the joint effects of both seed and pollen flow. Here we examined the effects of seed and pollen flow on shaping a species' distribution in one-dimensional space. Our results demonstrate that pollen flow can enhance range expansion when immigrating genes are adaptive to recipient populations, but can shrink a species' range when immigrating genes are maladaptive. The incompletely purging of maladaptive genes from immigrating pollen grains at the gametophyte stage can reinforce the biological barrier to range expansion. The linkage disequilibria attained by immigrating seeds and pollen grains indirectly amplify the effects of the reaction component and further limit a species' range. The cumulative effect from multiple loci each with a small effect can be substantial on altering a species' range when these genes are maladaptive. These theoretical predictions can help understand the role of pollen flow that is incapable of colonizing new habitats in range expansion.
Gene Flow↗
Hierarchical patterns of global human Y-chromosome diversity.
We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For example, populations from Central Asia had the highest levels of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of the total variance of NRY haplotypes was attributable to differences among populations (i.e., Phi(ST) = 0.36). When a series of AMOVA analyses was performed on different groupings of the 50 populations, high levels of among-groups variance (Phi(CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three population groupings formed distinct clusters in multidimensional scaling plots. A nested cladistic analysis (NCA) demonstrated that both population structure processes (recurrent gene flow restricted by isolation by distance and long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explaining this tripartite division of global NRY diversity. As in our previous analyses of smaller NRY data sets, the NCA detected a global contiguous range expansion out of Africa at the level of the total cladogram. Our new results support a general scenario in which, after an early out-of-Africa range expansion, global-scale patterns of NRY variation were mainly influenced by migrations out of Asia. Two other notable findings of the NCA were (1) Europe as a "receiver" of intercontinental signals primarily from Asia, and (2) the large number of intracontinental signals within Africa. Our AMOVA analyses also supported the hypothesis that patrilocality effects are evident at local and regional scales, rather than at intercontinental and global levels. Finally, our results underscore the importance of subdivision of the human paternal gene pool and imply that caution should be exercised when using models and experimental strategies based on the assumption of panmixia.
Africa South of the Sahara↗
Experimental studies of adaptation in Clarkia xantiana. II. Fitness variation across a subspecies border.
Because the range boundary is the locale beyond which a taxon fails to persist, it provides a unique opportunity for studying the limits on adaptive evolution. Adaptive constraints on range expansion are perplexing in view of widespread ecotypic differentiation by habitat and region within a species' range (regional adaptation) and rapid evolutionary response to novel environments. In this study of two parapatric subspecies, Clarkia xantiana ssp. xantiana and C. x. ssp. parviflora, we compared the fitness of population transplants within their native region, in a non-native region within the native range, and in the non-native range to assess whether range expansion might be limited by a greater intensity of selection on colonists of a new range versus a new region within the range. The combined range of the two subspecies spans a west-to-east gradient of declining precipitation in the Sierra Nevada of California, with ssp. xantiana in the west being replaced by ssp. parviflora in the east. Both subspecies had significantly higher fitness in the native range (range adaptation), whereas regional adaptation was weak and was found only in the predominantly outcrossing ssp. xantiana but was absent in the inbreeding ssp. parvifilora. Because selection intensity on transplants was much stronger in the non-native range relative to non-native regions, there is a larger adaptive barrier to range versus regional expansion. Three of five sequential fitness components accounted for regional and range adaptation, but only one of them, survivorship from germination to flowering, contributed to both. Flower number contributed to regional adaptation in ssp. xantiana and fruit set (number of fruits per flower) to range adaptation. Differential survivorship of the two taxa or regional populations of ssp. xantiana in non-native environments was attributable, in part, to biotic interactions, including competition, herbivory, and pollination. For example, low fruit set in ssp. xantiana in the east was likely due to the absence of its principal specialist bee pollinators in ssp. parviflora's range. Thus, convergence on self-fertilization may be necessary for ssp. xantiana to invade ssp. parviflora's range, but the evolution of outcrossing would not be required for ssp. parviflora to invade ssp. xantiana's range.
Adaptation, Biological↗
Genetic subdivision, glacial refugia and postglacial recolonization in the golden-striped salamander, Chioglossa lusitanica (Amphibia: urodela).
The golden-striped salamander (Chioglossa lusitanica) is an ecologically specialized species, endemic to north-western Iberia. Patterns of genetic variation were assessed at seven polymorphic enzyme loci and one mitochondrial DNA (mtDNA) marker (cytochrome b) in 17 populations across its range. Estimates of enzyme genetic diversity revealed a high degree of genetic subdivision (FST = 0.68), mainly attributable to the existence of two groups of populations. The groups were located, respectively, north and south of the Mondego River, indicating that this river coincided with a major historical barrier to gene flow. A significant decrease in genetic variability from the Mondego northwards was associated with the Douro and Minho rivers. mtDNA sequence variation revealed a congruent pattern of two haplotype groups (d = 2.2%), with a geographical distribution resembling that of allozymes. The pattern and depth of genetic variation is consistent with the following hypotheses: (i) subdivision of an ancestral range of the species prior to the middle Pleistocene; (ii) secondary contact between populations representing historical refugia; (iii) relatively recent range expansion giving rise to the northern part of the species range; and (iv) loss of genetic variation through founder effects during range expansion across major rivers.
Alcohol Dehydrogenase↗
Patterns of spatial genetic structuring in a hydropsychid caddisfly (Cheumatopsyche sp. AV1) from southeastern Australia.
We assessed levels of mitochondrial genetic spatial structuring in the hydropsychid caddisfly Cheumatopsyche sp. AV1 in southeastern New South Wales, Australia. No significant spatial structuring was detected within or between catchments using analysis of molecular variance, and nested clade contingency analysis suggested no strong relationship between haplotypes and geographical location, at any clade level. However, tests for association among haplotypes incorporating geographical distance in the nested clade analysis, revealed patterns of historical range expansion and recent restricted gene flow. Most likely, population fragmentation preceded range expansion, although subsequent recontact and gene flow among the previously sundered populations has apparently obscured the geographical signature of the former fragmentation. Taken together, our analyses suggest that a number of populations fragmented during the Pleistocene evolved in isolation for a time and subsequently expanded into secondary contact. Since expansion, there has apparently been substantial (albeit somewhat restricted) dispersal and gene flow of adult female Cheumatopsyche sp. AV1, throughout the study area.
Analysis of Variance↗
Intra-deme molecular diversity in spatially expanding populations.
We report here a simulation study examining the effect of a recent spatial expansion on the pattern of molecular diversity within a deme. We first simulate a range expansion in a virtual world consisting in a two-dimensional array of demes exchanging a given proportion of migrants (m) with their neighbors. The recorded demographic and migration histories are then used under a coalescent approach to generate the genetic diversity in a sample of genes. We find that the shape of the gene genealogies and the overall pattern of diversity within demes depend not only on the age of the expansion but also on the level of gene flow between neighboring demes, as measured by the product Nm, where N is the size of a deme. For small Nm values (< approximately 20 migrants sent outwards per generation), a substantial proportion of coalescent events occur early in the genealogy, whereas with larger levels of gene flow, most coalescent events occur around the time of the onset of the spatial expansion. Gene genealogies are star shaped, and mismatch distributions are unimodal after a range expansion for large Nm values. In contrast, gene genealogies present a mixture of both very short and very long branch lengths, and mismatch distributions are multimodal for small Nm values. It follows that statistics used in tests of selective neutrality like Tajima's D statistic or Fu's F(S) statistic will show very significant negative values after a spatial expansion only in demes with high Nm values. In the context of human evolution, this difference could explain very simply the fact that analyses of samples of mitochondrial DNA sequences reveal multimodal mismatch distributions in hunter-gatherers and unimodal distributions in post-Neolithic populations. Indeed, the current simulations show that a recent increase in deme size (resulting in a larger Nm value) is sufficient to prevent recent coalescent events and thus lead to unimodal mismatch distributions, even if deme sizes (and therefore Nm values) were previously much smaller. The fact that molecular diversity within deme is so dependent on recent levels of gene flow suggests that it should be possible to estimate Nm values from samples drawn from a single deme.
Animals↗
Nonuniform vertical and horizontal setting expansion of a phosphate-bonded investment.
PURPOSE: This study developed a new device for measuring the internal setting expansion of phosphate-bonded investment and assessed the effect that different pattern materials may have on the internal setting expansion. MATERIAL AND METHODS: The measuring device consisted of 2 horizontal plungers, a vertical needle, 2 digital dial gauges, and a protection tube with a disk. Outward displacement of the 2 horizontal plungers by investment setting expansion was transmitted to a digital dial gauge through the vertical needle. Upward displacement of a protection tube was measured by another digital dial gauge. Three pattern materials, including soft and hard inlay waxes and an autopolymerizing resin, were used. Data were analyzed with ANOVA and Scheffe's F test for all post hoc pairwise comparisons (95% confidence level). RESULTS: For all pattern materials, vertical setting expansion (range of means, 2.26% to 2.73%) was significantly higher than the horizontal setting expansion (range of means, 0.09% to 1.50%) (P <.05). In addition, for the hard inlay wax pattern, the horizontal setting expansion for the cervical aspect (means, 1.39%) was significantly higher than that of the occlusal aspect (means, 0.54%) (P <.05). CONCLUSION: In this study, the new measuring device was a convenient and reliable method for quantitative assessment of internal setting expansion. Regardless of the type of pattern material, a phosphate-bonded investment caused nonuniform setting expansion, especially in a horizontal direction, which lead to the distortion of the pattern.
Analysis of Variance↗
Phylogeography of the coronulid barnacle, Chelonibia testudinaria, from loggerhead sea turtles, Caretta caretta.
The barnacle, Chelonibia testudinaria, is a common inhabitant of the marine turtle epibiont community and plays a key role in the development of this community. Phylogeographic analysis of 79 cytochrome c oxidase I (COX1) sequences for barnacles collected from five populations found contrasting patterns of divergence for populations in the Atlantic vs. the Pacific Ocean. Our analysis indicates that the two Pacific populations, Senri Beach, Japan and Bahia Magdalena, Mexico, were not only highly divergent from the Atlantic populations but are highly divergent from one another. We suggest that barnacles from these populations may represent cryptic species. In contrast, sequence divergence was greatly reduced among barnacles collected from Wassaw Island, GA, USA, Keewaydin, FL, USA, and Kyparissia, Pèloponnésus Island, Greece. A reduction in sequence diversity at the latter site was attributed to a recent range expansion into the Mediterranean Sea. We examined historical patterns of migration among the three Atlantic and Mediterranean populations using the program migrate. This analysis indicates a high rate of migration from Keewaydin to Wassaw Island, contrasted with a much lower rate of migration in the opposite direction. The estimated migration rate from Kyparissia to Keewaydin was also non-negligible. We suggest that the association between C. testudinaria and loggerhead turtles and the patterns of turtle migration have played key roles in the expansion of the range of C. testudinaria into the Mediterranean Sea and the subsequent patterns of barnacle migration. We further propose that the difference between ocean basins, with respect to the impact of host migration on barnacle gene flow, probably stems from the fact that host-mediated dispersal in the Atlantic depends on advanced stage juveniles and adults while any host-mediated dispersal in the Pacific would have to involve early "pelagic" stage juvenile loggerheads.
Animal Migration↗
Molecular phylogeny and geography of Korean medaka fish (Oryzias latipes).
The phylogeny and geography of the medaka (Oryzias latipes) populations of Korea were investigated by analyzing sequence data for the mitochondrial control region. From the 41 haplotypes including 25 Korean haplotypes detected in 64 Korean specimens and data for the Japanese and Chinese populations, phylogenetic and nested clade analyses were executed to examine the phylogeny of haplogroups and the relation of the genetic architecture of the haplotypes to the historical geography of the Korean medaka fish. The analyses suggest that there are two very distinct lineages of Korean medaka, and that these result from reproductive isolation mechanisms due to geographic barriers. The southeastern lineage has experienced recent range expansion to the western region. The northwestern lineage, sister to Chinese populations, showed evidence of internal range expansion with shared haplotypes.
Animals↗
Geographic patterns of genetic differentiation within the restricted range of the endangered Stephens' kangaroo rat Dipodomys stephensi.
Using mtDNA variation in the kangaroo rat Dipodomys stephensi, we found no support for the hypothesis that a species with an historically restricted range will exhibit low levels of genetic polymorphism and little genetic structure. Dipodomys stephensi has long been restricted to a few interior coastal valleys in southern California encompassing an area of approximately 70 x 40 km; however, we found high levels of genetic variation over much of its range and significant genetic structure both within and between regions. We also found evidence for a recent range expansion. Dipodomys stephensi is a federally endangered species that is separated from D. panamintinus, its presumed sister taxon, by a mountain range to the north. We assessed genetic variation by sequencing 645 bases of the mitochondrial d-loop from 61 individuals sampled from 16 locations across the species range and rooted their relationship using two D. panamintinus individuals. Despite its limited geographic range, the level of mtDNA variation in D. stephensi is comparable to that of other rodents, including that of the more widely distributed D. panamintinus. This variation revealed significant regional differentiation. The northern, central, and southern regions of the range differ in both the level and the distribution of genetic variation. Phylogenetic analysis revealed that the center of the range contains the most diversity of lineages, including the most basal. In this region and in the north, most haplotypes were found at only a single location (25/29), or at a pair of nearby locations (3/29). In addition, related haplotypes clustered geographically. These results are consistent with long-term demographic stability characterized by limited dispersal and high local effective population size. Further support for this conclusion is the finding of unique diversity in two northern peripheral populations, Norco and Potrero Creek (PC). However, in sharp contrast, one haplotype (CC) was found at five of 11 central and northern locations and comprised 18% of individuals sampled. The atypical distribution of the CC haplotype reflected a pattern seen more strongly in the southern region. Here the CC haplotype comprised 69% of the sample and was found at all five sampling locations. Consequently, the southern region had very low genetic variability. We propose that this dominance of CC was probably due to a local population bottleneck that occurred during a recent range expansion into the southern region.
Animals↗
Nested clade analysis and the genetic evidence for population expansion in the phylogeography of the golden-striped salamander, Chioglossa lusitanica (Amphibia: Urodela).
The golden-striped salamander, Chioglossa lusitanica, is a streamside species distributed in the northwest of the Iberian Peninsula. We gathered cytochrome b mitochondrial DNA sequence data from samples across the species range and used nested clade distance analysis to assess evolutionary processes explaining the geographical distribution of mtDNA diversity in Chioglossa lusitanica. A significant association was observed between genetic structure and geography. The geographical patterns were explained by past fragmentation and restricted gene flow. Inferences were concordant with previous hypotheses (from allozyme data) involving an old fragmentation event and secondary contact near the Mondego River in central Portugal. A range expansion to the north from a southern refuge was supported by descriptive interpretations of mtDNA data and by complementary analyses suggesting population expansions, but not by formal nested clade analysis. The power of nested clade analysis to detect the genetic signature of range expansion deserves further testing.
Animals↗
Phylogeography and population history of Atlantic mackerel (Scomber scombrus L.): a genealogical approach reveals genetic structuring among the eastern Atlantic stocks.
Despite the resolving power of DNA markers, pelagic and migratory marine fish species generally show very little geographical population structuring. In mackerel (Scomber scombrus L.) population differentiation has been detected only at a transatlantic scale. By applying two regions in mitochondrial DNA (mtDNA) (D-loop and cytochrome b (cytb)) in combination with genealogical and frequency-based statistical approaches, our data suggest population differentiation among eastern Atlantic spawning stocks. In contrast, and indicative of homing behaviour, no genetic structuring was observed among shoals of individuals outside the spawning season. Among spawning stocks, mtDNA D-loop sequences detected differentiation within the eastern Atlantic, while the cytb gene detected transatlantic differentiation. The impact of recurrent events (e.g. gene flow restricted by isolation by distance) and historic events (e.g. population range expansions) among spawning stocks was investigated applying a nested cladistic analysis of geographical distribution of cytb haplotype lineages. In the eastern Atlantic, historical population range expansion, presumably in connection with recolonization of northern areas after the last glaciation, is suggested to be the main factor determining mtDNA lineage distribution. This was supported by estimates of mtDNA nucleotide diversity, where the highest diversity was observed for the stock spawning in the Bay of Biscay, for which the size estimate is only 15% of the largest stock (Celtic Sea). In addition to revealing population differentiation, our data demonstrate the importance of sampling strategy and the power of applying statistical methods addressing both ongoing and historical population processes.
Animals↗