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Historical Demography and Present Day Population Structure of the Greenfinch, Carduelis chloris-An Analysis of mtDNA Control-Region Sequences
Abstract
Genetic variability within and among 10 geographically distinct populations of Greenfinches (Carduelis chloris) was assayed by directly sequencing a 637 BP part of the mtDNA control region from 194 individuals. Thirteen variable positions defined 18 haplotypes with a maximum sequence divergence of 0.8% Haplotype (h = 0.28-0.77) and nucleotide (pi = 0.058-0.17%) diversities within populations were low, and decreased with increasing latitude (h:r(s) = -0.81; pi: r(s) = -0.89). The distribution of pairwise nucleotide differences fit better with expectations of a ''sudden expansion'' than of an ''equilibrium'' model, and the estimates of long term effective population sizes were considerably lower than current census estimates, especially in northern European samples. Selection is an unlikely cause of observed patterns because the distribution of variability conformed to expectations of neutral infinite alleles model and haplotype diversity across populations was positively correlated with heterozygosity !HE) in nuclear genes (I; = 0.74, P < 0.05). Hence, a recent bottleneck, followed by serial bottlenecking during the process of post-Pleistocene recolonization of northern Europe, together with recent population expansion provide a plausible explanation for the low genetic diversity in the north. Genetic distances among populations showed a clear pattern of isolation-by-distance, and 14% of the haplotypic variation was among populations, the rest being distributed among individuals within populations. In accordance with allozyme and morphological data, a hierarchical analysis of nucleotide diversity recognized southern European populations as distinct from northern European ones. However, the magnitude of divergence in mtDNA, allozymes and morphology were highly dissimilar (morphology > mtDNA > allozymes).
... For events of secondary contact, an increase in genetic diversity in the population that received more migrants is expected, since migrants are likely to carry new alleles to the receiver population (see [26]). On the other hand, colonization events from a core population lead to a gradual reduction in genetic diversity towards newly colonized areas due to genetic drift operating through repeated founder events or bottlenecks [24][25][26][27]. Additionally, when the equilibrium between migration and genetic drift is reached, patterns of genetic diversity may be also explained by the isolation-by-distance model, in which geographically close individuals tend to be genetically more similar than individuals that are further apart [28,29]. ...
... Considering that areas of greater genetic diversity are commonly associated with the origin center of a species (e.g. [25,27,76]), it is plausible to assume that the origin center of the N. fasciata lineage is in the southern part of the Cerrado. The southern Cerrado encompasses some topographical relief core areas, such as Parecis, Paraná-Guimarães and Serra da Canastra plateaus, which are, at least in part, concordant with some predicted stable areas (see Fig 3). ...
... These results suggest that these populations were partially isolated before the expansion event. Events of population expansion may result in a gradual reduction in genetic diversity toward newly colonized areas due to successive founder effects (leadingedge expansion model) and the increase in genetic diversity in populations that received Phylogeography of the White-banded Tanager migrants [26,27]. Thus, our results indicate that the process of population expansion promoted the reestablishment of gene flow in the southern part of the species distribution, reconnecting genetic groups historically isolated in different plateaus (Fig 3). ...
We performed phylogeographic and genetic structure analyses of Neothraupis fasciata joined with species distribution modelling to evaluate whether: (1) the distribution of genetic variability shows a pattern expected by the isolation-by-distance model; (2) the influence of the Pleistocene climate changes on species distribution; and (3) climate/climatic stability (hypothesis of climatic stability) as a predictor of population genetic diversity. Based on two molecular datasets (ND2 and FIB-5), the isolation-by-distance hypothesis was not supported. The mitochondrial haplotype network indicated the existence of historically isolated populations at the southern range of the species distribution, and recent population expansion was identified by both neutrality tests and extended Bayesian skyline plot analysis. Thus, the climatic changes during the Pleistocene might have promoted the reconnection of the partially isolated southern populations, which may have persisted in the plateaus during the cycles of savanna contractions. Subsequently, this species (re)colonized northern areas of the species present distribution, following the continuous vegetation on the São Francisco and Central plateaus about 60 kyr, and also reached the Amazonian savannas likely via the central corridor. Thus, our results indicated that the intrinsic relationship between the relief heterogeneity (plateaus and depressions) and the climatic fluctuations, mainly in the Pleistocene, promoted population reconnection and demographic expansion of N. fasciata.
... Numerous studies of temperate birds across a range of habitat types provide evidence of low genetic diversity due to population bottlenecking in glacial refugia, followed by rapid post-glacial (recent) population expansions (e.g. Zink and Dittman 1993;Merila et al. 1997;Fry and Zink 1998;Pestano et al. 2000). Similar patterns are also evident among tropical seabirds (Peck and Congdon 2004) and some tropical forest species (Brook et al. 1997;Bowie and Fjeldsa 2004) not directly impacted by ice sheets. ...
... Therefore, to obtain accurate approximation of the period during which any expansion may have occurred I used two different mutation rates. Firstly, I used a μ value of 14.8%, in accordance with the rate calculated for the same mtDNA control region Part I and II in greenfinch (Merila et al. 1997) and dunlin (Wenink et al. 1996). This is a standard value of μ used in numerous previous studies to calculate expansion coefficients of this type. ...
... Fringilla teydea (Pestano et al. 2000), but high relative to others, such as the blackfaced spoonbill Platalea minor (Yeung et al. 2006 Pavlova et al. (2005) and ~10% of that found in the greenfinch Carduelis chloris (0.13, range 0.11-0.15, CR; Merila et al,(1997). ...
The problem of how to conserve small and declining populations is currently receiving considerable attention in the ecological literature, particularly through the theoretical development of conservation biology and its application to endangered species conservation. This is true despite basic information on the natural history of most endangered species being very limited; not only for species that are very rare, elusive or living in remote areas, but also for species which occupy more accessible habitat (i.e. cultivated areas), such as the Java sparrow (Padda oryzivora).
In the research outlined in this thesis, field studies and molecular analyses were combined to establish the current population status, level of continued threat, contemporary connectivity among remnant populations and the genetic diversity of the endangered Java sparrow. Field work included intensive censuses at 6 sites across Central and East Java during the 2004 and 2005 breeding seasons. To gain information about the current scale of trading and trafficking of Java sparrows, the numbers of birds for sale were surveyed at 7 bird markets, mostly situated close to the bird census sites. Further interviews with bird trappers established the level of trapping and distribution of trapping sites.
DNA was extracted from both fresh whole blood (field samples) and tissue samples (museum specimens) and analysed using two different molecular marker systems – part one and two of the mtDNA control region and 5 independent nuclear microsatellite loci. MtDNA sequence data were used to infer phylogeography and historical demography of the Java sparrow, while, multi-locus microsatellite genotyping was used to assess contemporary connectivity and levels of genetic variation. In order to predict the future fate of the Java sparrow, a PVA and sensitivity analysis was also undertaken. Stochastic modelling was carried out using the program VORTEX.
The results of this study highlight that remnant populations of Java sparrow in Central and East Java are currently small and highly fragmented. Based on roost counts at 6 sites, population estimates range from 5.8 (± 0.2 SE) to 125.2 (± 1.7 SE). The total estimated population for Central and East Java did not exceed 1000 individuals. If other regions of Indonesia within the species’ natural range have similar abundances, then the total Java sparrow population in Indonesia is likely to be at the lower end of the range of 2500 – 10,000 individuals that is currently used to classify the species as ‘Vulnerable’. The major threat from trapping and trading is still ongoing at a high level, with an average 59.3 % of the total population estimates being trapped during the study period. This threat is particularly severe in central Java, where market demands were mainly supplied by local wild caught birds. In contrast, in the east Java bird markets, introduced and captive bred birds were substituted to satisfy high market demand. These findings emphasize the potential abundance of Java sparrows that may occur in currently unstudied introduced populations on outer islands (e.g. Kalimantan), and the important role that introduced and captive bred birds currently have in mitigating further declines. They also highlight the potential usefulness of these introduced populations as part of future conservation schemes for the Java sparrow.
Analysis of mtDNA sequence data was used to infer the effects of historic habitat changes on population demography and genetic diversity in the Java sparrow. Despite an expectation that this species would have increased habitat availability during glacial maxima, analysis based on standard mtDNA mutation rates revealed that major climatic shifts have caused bottlenecking in Java sparrows similar to those observed in temperate species impacted by expanding ice sheets. Alternatively, using more recently derived and contrasting mtDNA mutation rates suggests the Java sparrow was bottlenecked during the expansion of rainforest in the early Holocene, and likely expanded during deforestation associated with the arrival of cultivation to Java. If correct, this finding adds to an increasing number of studies highlighting the impact of human colonization on the distribution and abundance of endemic species.
Microsatellite genotyping demonstrated that genetic variation in remnant Java sparrow populations was low, in the middle range of genetic variation observed for other endangered species. Levels of diversity among contemporary populations did not differ from historic samples. In addition, significant structuring was found among remnant but not historic populations, implying recent fragmentation and limited current inter-population movement. Therefore, it is likely that while recent population declines have, as yet, had limited impact on genetic diversity, they have had a significant impact on levels of inter-population gene flow.
Stochastic PVA modelling suggested that, under a best case scenario, Java sparrows would be able to recover. Sensitivity analysis revealed that the PVA models were most sensitive to mortality and fecundity schedules. However, the results highlighted that further field studies of these parameters are necessary to gain a more realistic assessment of the potential fate of the Java sparrow over both the short and longer term. PVA also suggested that if the current level of trapping continues Java sparrow will become extinct within a very short period of time. Given that terminating trapping seems an unlikely short-term management option, these findings highlight the immediate need to formulate a trapping/harvesting strategy that minimizes the risk of extinction.
The implications of the results of this research are as follows: 1. It is proposed that the conservation status of Java sparrow to be transferred from Vulnerable to Endangered (A2a,b,d; E). This research also provides a more robust, high quality data set that can be used for conservation status assessment. 2. Trapping remains the main threatening process and must be reduced before other conservation measures can be effective. The use of captive bred and/or introduced birds should be encouraged to meet market demands. Further population studies on introduced populations (e.g. in Kalimantan) are a necessity to develop the sustainable use of these resources. 3. For management purposes the Java sparrow can be considered as a single Management Unit. However, to develop a sound conservation strategy for this species, it is important to take into account the concept of “ecological exchangeability”. For this purpose we need studies of behaviour, life history, and morphology relative to environment. Such studies will allow more meaningful assessment of biologically relevant differentiation among the remnant populations of the Java sparrow. 4. There is also a need for further research on demographic parameters and breeding biology to gain more realistic predictions of population viability. 5. There is a critical short-term need to formulate a trapping/harvesting strategy to minimize the extinction risk. Working thresholds need to be established as a short-term management priority and as a basis for more effective and sustainable management strategies over the longer term.
... Adopting a very low divergence rate of 2% per million years, : equates to 8.5 x 10 -7 (assumes a generation time of 6 years for threadfin). Adopting the highest recorded divergence rate for the control region in vertebrates (32% per million years; Merilä et al. 1997), : = 1.6 x 10 -6 . Thus, it is likely that the female effective size of the Pacific threadfin population at present is between approximately 205,000 and 385,000 individuals. ...
... The sum of square deviations between the observed and expected distributions (SSD = 0.0008) was not significantly different (P = 0.66) from a simulated distribution that assumes that the estimated parameters ϑ, 1 0 , and 1 1 are the true ones (see Schneider and Excoffier, 1999). The mean square error (MSE) measuring the fit of the data to the sudden expansion model was 0.001131 whereas the MSE measuring its fit to an "equilibrium" (no growth) model was 0.050125 (see Merilä et al., 1997). Harpending's raggedness index was very low (r = 0.007), indicating that the observed distribution was unimodal. ...
... The BGL staff obtains both the mtDNA and microsatellite genotypes of all female red drum and the microsatellite genotypes of all male red drum held at SERF for potential use as broodstock. In red drum mtDNA maternity studies, which involved >1000 offspring and 14 broodstock mothers, BGL staff found no instances where the mtDNA genetic-tag sequences of the mothers and their offspring differed (unpublished data), nor do they expect to find any in the future, based on reported mutation rates for the mtDNA control region (Merilä et al., 1997). Thus, because of the unique mode of inheritance of mtDNA, the mtDNA genotypes of the broods are known if the mtDNA genotypes of the female broodstock are known. ...
... Haplotypes differed from one another by 1-7 substitutions in 1144 bp (0.09% to 0.64%). Overall, mean pairwise divergence among haplotypes in the Bering region was 0.36% (SD = 0.17%, n = 78 comparisons), comparable to the level of variation in greenfinches (Carduelis chloris) across Europe (0.39%; Merilä et al. 1997). This level of divergence was similar to that among the endemic Aleutian Island haplotypes alone (mean ± SD = 0.38% ± 0.16%, n = 21 comparisons). ...
... Not only were Aleutian Islands haplotypes unique, the total haplotypic diversity (h) of this region (Aleutian populations pooled) was twice that of mainland Alaskan and Siberian populations combined (Table 2). Overall, haplotypic diversity of all populations pooled was 0.65, which is moderate relative to levels of haplotypic diversity in this part of the control region in other bird species (Baker & Marshall 1997;Merilä et al. 1997). Nucleotide diversity within the Aleutian Islands as a group was almost 10 times that in mainland Alaska and Siberia combined. ...
... Typically, lower levels of genetic diversity are found among populations in a recently glaciated area than among populations that have persisted in a nonglaciated region for a much longer period. For example, gradients in levels of genetic variability have been found in greenfinches (Merilä et al. 1997) and humans (Homo sapiens; Tishkoff et al. 1996), wherein haplotype diversity was highest in tropical and south temperate regions, and much lower in the formerly glaciated northern latitudes. In contrast to this general pattern, haplotype and nucleotide diversity is much higher in Aleutian rock ptarmigan (which have been established for less than 11 000 years), than in mainland populations that occupy formerly nonglaciated mainland sites in Alaska and Siberia. ...
In this paper, we address alternative hypotheses for the evolution of subspecies of rock ptarmigan (Lagopus mutus) endemic to the Aleutian Archipelago. To do this we examined patterns of genetic differentiation among populations of rock ptarmigan in the Aleutian Islands and parts of both Alaska and Siberia. Variation in mitochondrial control region sequences of 105 rock ptarmigan from 10 subspecies within the Bering region revealed three major phylogenetic lineages, two of which are endemic to the Aleutian Islands. Accordingly, haplotype and nucleotide diversities of rock ptarmigan within the archipelago are much higher than within mainland Alaska or Siberia. For Aleutian rock ptarmigan, analyses of molecular variance indicated significant genetic structuring and low estimates of gene flow among populations, despite small interisland distances within the archipelago. However, isolation by distance did not describe the pattern of gene flow or differentiation at this scale. Our estimates of divergence times of lineages suggest that Aleutian rock ptarmigan became isolated prior to the most recent Pleistocene glaciation event (late Wisconsin Stade) and that current patterns of genetic variation reflect the postglacial redistribution of divergent lineages and subsequent limited gene flow. In addition, genetic divergence among lineages was concordant with the distribution of plumage types among subspecies. The patterns of genetic variation described here for rock ptarmigan provide evidence for the role of glacial vicariance in contributing to genetic diversity within this and other Bering region species.
... In Europe, southern peninsulas (i.e. Iberia, Italia, Balkans, and Anatolia) served as refugial areas for many bird species (Merilä et al. 1997, Bensch & Hasselquist 1999, Griswold & Baker 2002, Brito 2005, Perktas et al. 2011, Perktaş & Quintero 2013. Our results from phylogeography, together with ecological niche modelling, revealed additional new insights into the historical demography of the Eurasian green woodpecker. ...
... This pattern was thus in accordance with Avise's phylogeographic category IV (Avise 2000), which refer to shallow gene trees and sympatric linages refer to expansion events from small or modest number of founders (e.g. Merilä et al. 1997). Therefore, this result might not provide enough evidence of multiple glacial refugia. ...
In this study, we re-evaluated historical demography of the Eurasian green woodpecker (Picus viridis) on the basis of previously published multi-locus mitochondrial DNA (mtDNA) data and ecological niche modelling. We particularly aimed to test glacial refugia hypothesis during climatic oscillations of the late Quaternary for the Eurasian green woodpecker. Our results indicate that the Eurasian green woodpecker was sensitive to the effects of climate change. Prior to the Last Glacial Maximum (22000 years ago), the population contraction started and the Eurasian green woodpecker restricted its range to southern Europe (including France), Anatolia, and the Caucasus/Caspian region, and, afterwards, substantially expanded its range from this restricted area to its present range around 14500 years before present. Therefore, during the Last Glacial Maximum, we recognize a single large refugium for this species, located in southern Europe (including France), Anatolia, and the Caucasus/Caspian region.
... Several authors [1,3,[6][7][8][9][10][11][12] have addressed the relationship between modern species in glaciated environments and glacial refugia. Phylogeographic studies in both Europe and North America have shown substantially less heterozygosity in populations of terrestrial nonhuman mammals [7,12], birds [8], and a semiaquatic amphibian [11] in glaciated regions compared to unglaciated regions, supporting the hypothesis of relatively recent invasions into glaciated environments. ...
... Several authors [1,3,[6][7][8][9][10][11][12] have addressed the relationship between modern species in glaciated environments and glacial refugia. Phylogeographic studies in both Europe and North America have shown substantially less heterozygosity in populations of terrestrial nonhuman mammals [7,12], birds [8], and a semiaquatic amphibian [11] in glaciated regions compared to unglaciated regions, supporting the hypothesis of relatively recent invasions into glaciated environments. It is expected that the origins of range expansion are in the direction of increased genetic diversity. ...
Spatial distributions of crayfish were evaluated in relation to glacial geography and possible modes of dispersal from refugia. Species dispersal patterns were a priori hypothesized and tested using principle components analysis (PCA). PCA factor loading plots were evaluated for hypothesized crayfish dispersal patterns. Cambarus laevis was limited to the unglaciated region, while Orconectes immunis, Orconectes virilis, and Procambarus gracilis may have dispersed from western glacial refugia in the upper Missouri drainage. Fallicambarus fodiens and Procambarus acutus dispersed from south of the glacial advance within the Mississippi embayment. Previous dispersal hypotheses for Orconectes propinquus recognized that northern refugia may have been from the Driftless Area in Wisconsin and Illinois and may have invaded more than one refuge since this species was common in unglaciated areas of southwestern Indiana. Orconectes indianensis center of abundance is in the unglaciated region. Disjunct populations likely dispersed into temporary glacial lakes that, when receded, left populations in previously glaciated areas. Cambarus polychromatus possibly dispersed from southern refugia, while Cambarus sp. A cf. diogenes dispersed from southern refugia not sympatric with C. polychromatus. The glacial refugia included western and southern areas of the glacial maximum; however, northern dispersal routes may be important with global climate change.
... These demographic changes (or lack thereof) can then be related to environmental and lifehistory characteristics of populations. Historical demography has figured prominently in evolutionary studies of one or a few species (Merilä et al. 1997;Bos et al. 2008; species (e.g., those confined to an island), yet they are close enough to North America to support large numbers of wintering migrants (Ricklefs and Bermingham 2008a). Among the West Indies, Hispaniola ( Fig. 1) has the highest number of bird species, including *95 North American migrants, *105 breeding resident species, and 31 endemic species (Latta et al. 2006). ...
... Rogers and Harpending (1992) showed that historical changes in population size can affect the genetic diversity of a population, and that information about population history can be extracted from DNA sequences. Many subsequent studies have illustrated the ability of contemporary DNA sequences to provide insight into the dynamics of historical populations (Merilä et al. 1997;Bos et al. 2008;Hawley et al. 2008;Lerner et al. 2009;Norgate et al. 2009;Reding et al. 2010;Qu et al. 2010). We evaluated molecular signatures of historical demography using mismatch distributions and demographic statistics. ...
Islands offer unique opportunities for studies of evolution and historical demography. We hypothesized that wintering North American migrant bird species would show genetic evidence of population expansion over recent millennia due to the expansion of their breeding distributions following the retreat of the Laurentide ice sheet. In contrast, we presumed that non-migratory species would exhibit more stable historical demographies. We used mtDNA sequences from 649 individuals of 16 avian species on the Caribbean island of Hispaniola to test this prediction. Mismatch distributions did not differ significantly between migrants and non-migrants. However, neutrality indices indicated population expansion in the migrant species, as well as two non-migratory resident species with extensive distributions. Evidence of population expansion was less consistent in other non-migratory residents. We infer that climate prior to the Last Glacial Maximum significantly reduced effective population sizes of most migratory North American bird populations and some resident Hispaniolan bird populations. Our data further revealed that mismatch statistics were poorly correlated with and less informative than the neutrality test statistics, a consideration for future demographic studies.
... In China, the genus is listed under Class II of the nationally protected animals classification. Intraspecific phylogeographic patterns are useful for elucidating the spatio-temporal dynamics of a species' population size, dispersal history and extent of geographical isolation (Baker & Marshall, 1997;Merila et al., 1997;Zink, 1997;Kvist et al., 1999;Leonard et al., 2000;Zhang et al., 2005). Such patterns can thus provide a theoretical basis for species conservation. ...
Geological events and historical environmental change can strongly affect the genetic structures and differentiation of fish populations. Although the central region of the Yunnan-Guizhou Plateau contains the highest concentration of rift-subsidence lakes in China, the effects of key geological events on the distributions and genetic structures of the regional fauna remain poorly understood. Fishes of the genus Sinocyclocheilus are endemic to the Yunnan-Guizhou Plateau, where they are found in karst landforms. As a result of environmental pollution and other human activities, Sinocyclocheilus populations have decreased sharply, and the genus is currently listed under Class II of the nationally protected animals classification in China. Examining the phylogeographic patterns of Sinocyclocheilus fishes can be useful for elucidating the spatio-temporal dynamics of their population size, dispersal history and extent of geographical isolation, thereby providing a theoretical basis for their protection. Here, we used Restriction Site Associated DNA Sequencing (RAD-seq) to investigate the evolution of Sinocyclocheilus fishes. Our analysis supports the endemicity of Sinocyclocheilus, and identifies the formation of Dianchi Lake and Fuxian Lake as key geological events shaping Sinocyclocheilus population structure. We estimate that the most recent common ancestor (MRCA) of Sinocyclocheilus fish occurred in the Central Yunnan Basin 3.75~3.11 Ma. It is the first time to prove that the altitude change has a great influence on the genetic variation among the populations of Sinocyclocheilus. We discuss the implications of our results for the protection and management of Sinocyclocheilus grahami and other cave fishes.
... This pattern fits the general prediction of the maintenance of genetic diversity in glacial refugia and its loss during expansion into northern latitudes (Hewitt, 1999). The same is suggested by the star-like distribution of haplotypes, the unimodal mismatch distribution, and the negative Tajima's D and Fu's F S indices that are all typical of populations that experienced low numbers, followed by a sudden increase (Ball et al., 1988, Merilä et al., 1997. Hence, European lesser spotted eagles carry genetic signs of demographic and/or spatial expansion that occurred after a population bottleneck in the past. ...
Characterizing the genetic diversity and structure of populations is essential for understanding their evolutionary history and planning species conservation. The lesser spotted eagle (Clanga pomarina) is a large migratory raptor with a relatively small breeding range concentrated in Eastern Europe. We evaluated the level of genetic diversity and population structuring by estimating the length diversity of 23 microsatellite markers in 306 individuals and sequencing 473 nucleotides from the mitochondrial pseudo-control region in 265 individuals across the distribution range. The microsatellite data suggested shallow differentiation between geographical regions and moderate genetic diversity across the range; no recent population bottlenecks were detected. Mitochondrial diversity was relatively low; however, high values were recorded at the southern edge of the distribution range. This, in combination with the star-like distribution of mitochondrial haplotypes, suggests the expansion of the European population from a single (Balkan) refugium during the late Pleistocene or early Holocene after the glacial population bottleneck. However, the Caucasian population may have survived in a separate refugium. We conclude that the lack of clear population structuring and ongoing gene flow across Europe support the treatment of the geographically restricted global population of the lesser spotted eagle as a single evolutionary and conservation unit.
... In addition, if the isolated Amazonian savanna populations were derived from the Cerrado core domain, it is predicted that the new peripheral population will be phylogenetically embedded within its ancestral population (i.e., an apomorphic Amazonian population and a paraphyletic Cerrado, Figure 1a; see further explanation in Frey, 1993). Because the new population should have been founded from a small sample of individuals (founder effect), one would expect lower genetic diversity and a younger age for the new population than in the parental Cerrado population (Merilä et al., 1997). ...
The main objective of this study is to evaluate biogeographic hypotheses of diversification and connection between isolated savannas north (Amazonian savannas) and south (Cerrado core) of the Amazon River. To achieve our goal, we employed genomic markers (genotyping‐by‐sequencing) to evaluate the genetic structure, population phylogenetic relationships, and historical range shifts of four Neotropical passerines with peri‐Atlantic distributions: the Narrow‐billed Woodcreeper (Lepidocolaptes angustirostris), the Plain‐crested Elaenia (Elaenia cristata), the Grassland Sparrow (Ammodramus humeralis), and the White‐banded Tanager (Neothraupis fasciata). The population genetic analyses indicated that landscape (e.g., geographic distance, landscape resistance, and percentage of tree cover) and climate metrics explained divergence among populations in most species, but without indicating a differential role between current and historical factors. Our results did not fully support the hypothesis that isolated populations at Amazonian savannas have been recently derived from the Cerrado core domain. Intraspecific phylogenies and gene flow analyses supported multiple routes of connection between the Cerrado and Amazonian savannas, rejecting the hypothesis that the Atlantic corridor explains the peri‐Atlantic distribution. Our results reveal that the biogeographic history of the region is complex and cannot be explained by simple vicariant models.
... Phylogeographic studies are valuable in showing how populations responded to the late Pleistocene cycles of glaciation, especially in the northern hemisphere. For example, Merila et al. (1997) compared mtDNA sequences from populations of Greenfi nch (Carduelis chloris) distributed along a north-south transect in Europe. An unstructured haplotype phylogeny revealed no pattern of historical isolation. ...
We conducted phylogeographic analyses of Motacilla flava (Yellow Wagtail) and M. citreola (Citrine Wagtail). We analyzed mitochondrial DNA sequences from 167 M. flava specimens obtained from 17 localities throughout Eurasia and Alaska, and 38 specimens of M. citreola obtained from 7 Eurasian localities. Phylogenetic analysis revealed three clades within traditionally recognized M. flava: Europe and southwestern Asia, northeastern Eurasia, and southeastern Asia. Those groups should be considered species, because together they are not monophyletic, and are interspersed with M. citreola, M. cinerea, and M. alba. Motacilla citreola also is paraphyletic, consisting of two species-level groups. Northeastern and southeastern groups of M. flava each appear to be sister taxa to eastern and western groups of M. citreola, respectively. Together those four groups form a clade, whereas the western M. flava group is considerably more distant. Within each of the three groups of M. flava, and the two groups of M. citreola, little phylogeographic structure was detected. Signatures of past population expansion are evident for some populations of M. flava; expansion is more recent in Moscow, Kursk (western group), Yamal, and Anabar (northeastern group), and older in Tyva and Vyatka (western group). A history of population stability is inferred for the Yamal population of M. citreola. Nested-clade analyses detected contiguous range expansion for southeastern M. flava and restricted gene flow with isolation by distance for northeastern M. flava and eastern M. citreola.
... It is relatively easy, rapid, and inexpensive to sequence, and research work on rapidly evolving loci provides sufficient variation to draw inferences on the structure of populations [9][10][11][12]. The control region, also referred to as D-loop, often mutates faster than the rest of the mtDNA [12,13] and appears to be highly variable in birds [12,14]. Analysis of polymorphism in the Dloop region has proved to be informative in previous studies on genetic variation, structure, and phylogeography in birds [12,[15][16][17][18][19]. ...
We analyzed variations in 90 mitochondrial DNA (mtDNA) D-loop and heat shock protein 70 (HSP70) gene sequences from four populations of domesticated helmeted Guinea fowls (70 individuals) and 1 population of wild helmeted Guinea fowls (20 individuals) in Kenya in order to get information about their origin, genetic diversity, and traits associated with heat stress. 90 sequences were assigned to 25 distinct mtDNA and 4 HSP70 haplotypes. Most mtDNA haplotypes of the domesticated helmeted Guinea fowls were grouped into two main haplogroups, HgA and HgB. The wild population grouped into distinct mtDNA haplogroups. Two mtDNA haplotypes dominated across all populations of domesticated helmeted Guinea fowls: Hap2 and Hap4, while the dominant HSP70 haplotype found in all populations was CGC. Higher haplotype diversities were generally observed. The HSP70 haplotype diversities were low across all populations. The nucleotide diversity values for both mtDNA and HSP70 were generally low. Most mtDNA genetic variations occurred among populations for the three hierarchical categories considered while most variations in the HSP70 gene occurred among individuals within population. The lack of population structure among the domestic populations could suggest intensive genetic intermixing. The differentiation of the wild population may be due to a clearly distinct demographic history that shaped its genetic profile. Analysis of the Kenyan Guinea fowl population structure and history based on mtDNA D-loop variations and HSP70 gene functional polymorphisms complimented by archaeological and linguistic insight supports the hypothesis that most domesticated helmeted Guinea fowls in Kenya are related to the West African domesticated helmeted Guinea fowls. We recommend more molecular studies on this emerging poultry species with potential for poverty alleviation and food security against a backdrop of climate change in Africa.
... Previous genetic studies did not include many of the southern Spanish populations that comprise most of the distribution range of the species (Gante et al., 2009). This incomplete sampling is a handicap in the reconstruction of the evolutionary history of L. sclateri, as shown by other phylogeographic studies in which the studied species range was limited (Avise, 2000;Barraclough & Nee, 2001;Hourlay et al., 2008;King, Eackles, Gjetvaj, & Hoeh, 1999;Kvist, Martens, Ahola, & Orell, 2001;Marsh, Thakur, Bulka, & Clarke, 2004;Meril€ a, Bj€ orklund, & Baker, 1997). ...
Since the Cenozoic Era, the southern Iberian Peninsula has undergone a series of complex geological and climatic changes that have shaped the hydrographic configuration of the freshwater network, influencing the present-day distribution of primary freshwater species and favoring a high level of local endemicity. The cyprinid species Luciobarbus sclateri (Günther, 1968) is an endemic species confined to the southern Iberian Peninsula and characterized by a complex evolutionary history. Previous studies linked the structure of L. sclateri populations to the effects of climate change during glaciations and were not able to explain the genetic discordance found between nuclear and mitochondrial markers. The results of this study show that the structure of L. sclateri populations is a reflection of diversification processes linked to the geological history of the region. Thus, we found three main mitochondrial phylogroups: the first one corresponding to small basins in southern Iberian Peninsula, a second one in eastern Iberian Peninsula, corresponding to Segura population, and a third one including the rest of the basins where the species is distributed. The southern group began diverging in the Pliocene as result of tectonic dynamics characterized by the emersion of the basins around the Strait of Gibraltar. The other two groups began diverging with the formation of the current Iberian hydrographic system during Pleistocene. So, the isolation of the hydrographic basins was the main factor driving intraspecific differentiation, followed by recent secondary contacts, admixture, and re-isolation of the populations.
... There are only three independent estimates of the rate of mutation in the control region of birds: those for snow geese (Chen caerulescens, 20.8% per million years, domain I; Quinn 1992), Darwin's finches (Geospizinae, 5% per million years; Freeland 1997), and guillemots (Cepphus spp., domains II and III, 2% per million years; Kidd and Friesen 1998). Most published studies to date have based avian control region clocks on the snow goose mutation rate (e.g., Wenink et al. 1996;Merila et al. 1997) or on nonavian vertebrate mutation rates (Edwards 1997). Recalculating divergence times using the rate of mutation for the control region of Darwin's finches gives a mean divergence time for Nearctic rock ptarmigan lineages of 135,000 yr ago. ...
The glacial refugium hypothesis (GRH) proposes that glaciers promoted differentiation and generation of intraspecific diversity by isolating populations in ice-free refugia. We tested three predictions of this hypothesis for the evolutionary divergence of rock ptarmigan (Lagopus mutus) during the Wisconsin glaciation of the late Pleistocene. To do this, we examined subspecies distributions, population genetic structure, and phylogenetic relationships in 26 populations across North America and the Bering Sea region. First, we analyzed sequence variation in the mitochondrial control region, in a nuclear intron (Gapdh), and in an internal transcribed spacer (ITS1). Control region sequences of 154 rock ptarmigan revealed strong population and phylogeographic structure. Variation in intron sequences of 114 rock ptarmigan also revealed significant population structure compatible with results for the control region. Rock ptarmigan were invariant for ITS1. Second, we show that five known Nearctic refugia and an Icelandic refugium are concordant with the current distribution of morphologically distinct subspecies; five of these six refugia are geographically concordant with the distribution of closely related control region haplotypes. Third, our estimates of the time since phylogenetic lineages diverged predated the last glacial maximum for all but two lineages. In addition, all lines of evidence suggest that two unknown refugia in the Bering Sea region supported rock ptarmigan during the Wisconsin glaciation. Overall, our results are most consistent with the hypothesis that isolated populations of rock ptarmigan diverged in multiple refugia during the Wisconsin and that geographic variation reflects patterns of recolonization of the Nearctic after the ice receded. The GRH may therefore offer the most plausible explanation for similar biogeographic patterns in a variety of Nearctic vertebrates.
... Therefore, it is likely that the source pool of species from which the Caucasus avifauna originated was European. We note that many species are undifferentiated in their European ranges (Merilä et al. 1997, Griswold & Baker 2002, Salzburger et al. 2002, Päckert et al. 2003, Drovetski et al. 2004, Zink 2005, Bensch et al. 2006, Akimova et al. 2007, Saetre & Saethe 2010, Hung et al. 2012, Hung et al. 2013, Mettler et al. 2013, Rodrigues et al. 2013 ...
Organismal traits such as ecological specialization and migratory behavior may affect colonization potential, population persistence, and degree of isolation, factors that determine the composition and genetic structure of communities. However, studies focusing on community assembly rarely consider these factors jointly. We sequenced 16 nuclear and one mitochondrial genes from Caucasian and European populations of 30 forest-dwelling avian species that represent diverse ecological (specialist-generalist) and behavioral (migratory-resident) backgrounds. We tested the effects of organismal traits on population divergence and community assembly in the Caucasus forest, a continental mountain island setting. We found that (1) there is no concordance in divergence times between the Caucasus forest bird populations and their European counterparts, (2) habitat specialists tend to be more divergent than generalists, and (3) residents tend to be more divergent than migrants. Thus, specialists and residents contribute to the high level of endemism of Caucasus forest avifauna more than do generalists and migrants. Patterns of genetic differentiation are better explained by differences in effective population sizes, an often overlooked factor in comparative studies of phylogeography and speciation, than by divergence times or levels of gene flow. Our results suggest that the Caucasus forest avifauna was assembled through time via dispersal and/or multiple vicariant events, rather than originating simultaneously via a single isolation event. Our study is one of the first multi-locus, multi-species analyses revealing how ecological and migratory traits impact the evolutionary history of community formation on a continental island. This article is protected by copyright. All rights reserved.
... An alternative explanation to the incongruent pattern of molecular and morphological variation in flammea and cabaret is that adaptive evolutionary change in morphology occurred too recently for neutral mtDNA to diverge. Such a pattern is particularly likely to arise following a rapid population increase and range expansion from a bottlenecked population, a scenario that redpolls and many other species of higher latitudes have experienced after the retreat of the last ice age (Rogers 1995, Hewitt 1996, Merilä et al. 1997, Zink 1997. This is because neutral alleles are less likely to get lost due to genetic drift in growing populations (Otto & Whitlock 1997) whereas adaptive traits rapidly evolve in the newly colonised habitats (Schluter & Nagel 1995). ...
... Esta expansión relativamente rápida del área de distribución hacia latitudes septentrionales se debería a factores climáticos y a que la especie se ha habituado a pasar el invierno en área urbanas (Siverin, 1995). Así, los Carboneros que se expandieron hacia el norte durante las últimas décadas habrían llegado a hábitats nuevos para los cuales no estarían bien adaptados (Merilä et al., 1996;Merilä et al., 1997). Esto explicaría porque estas poblaciones de reciente llegada al norte del Paleártico occidental no tienen mayores tamaños de puesta que las del centro del Paleártico y además presentan un relativo peor éxito reproductor (Rytkönen & Orell, 2001). ...
En este trabajo se pretende mostrar como ciertos parámetros reproductores (fecha de puesta, tamaño de puesta) varían geográficamente (latitud, longitud, altitud, tipo de hábitat) en las especies de aves nidícolas e insectívoras. Para ello, se utiliza como especie modelo al Carbonero Común (Parus major). La fecha de puesta poblacional no difiere entre hábitats, no muestra relación con la longitud y se incrementa con la altitud. La fecha de puesta poblacional muestra una relación cuadrática con la latitud, con los valores más tempranos en latitudes medias. Por otro lado, el tamaño de puesta poblacional difiere entre los hábitats estudiados, siendo mayor en los bosques caducifolios, muestra una relación positiva con la longitud y una relación negativa con la altitud. Además, el tamaño de puesta poblacional muestra una relación cuadrática con la latitud, con los valores más altos en las latitudes intermedias. En el presente trabajo describimos que hipótesis han sido propuestas para intentar explicar por qué existen estos patrones en especies de aves nidícolas del Paleártico occidental.
... Fluctuations in population size reflect the idiosyncratic life-history characteristics of a given population, but concordant demographic fluctuations among species could also reflect long-term trends in environmental conditions. Many studies have considered the historical demography of a single species with a single marker (usually mtDNA, Merilä et al. 1997, Zink et al. 2006, Hawley et al. 2008, Lerner et al. 2009, Norgate et al. 2009, Brace et al. 2012). More recently, authors have used multiple markers to study individual species (Firestone et al. 1999, Tchaicka et al. 2007, Bos et al. 2008, Reding et al. 2010, Nietlisbach et al. 2012. ...
Molecular markers can be used to infer the demographic history of a given species, but many historic processes simultaneously impact multiple species. Thus, comparative historical demography has the potential to provide insight into drivers of evolution. In this study, we used nuclear DNA (nDNA) sequences to corroborate (or refute) demographic inferences based on earlier mitochondrial DNA (mtDNA) data from 16 species of Hispaniola birds. Our previously published analysis suggested population expansion in five of six migratory species (following glacial retreat in North America), with less evidence of expansion in non-migratory species. Additional molecular markers should reduce locus-specific bias, and so we generated sequence data for several nuclear loci. Test statistics associated with the nDNA provided only equivocal evidence for population expansion in 10 of the 16 species. Discordance between mtDNA and nDNA is not uncommon because the two genomes are exposed to different selective pressures and have different effective population sizes and modes of inheritance. The nDNA analyses reported here cast some doubt on our earlier mtDNA inferences. They also suggest that the signal to noise ratio of demographic statistics is typically low because of the inherent variability in selective regimes and coalescence across loci.
... The Pleistocene was characterized by global climatic perturbations, resulting in the development of large ice sheets and changes in the landscape and ecology of high-latitude continental areas of the northern hemisphere is the character of Pleistocene (Rising and Avise, 1993;Hewitt 1996;Merila et al., 1997). Range contractions and expansions have greatly influenced the level and distribution of intraspecific genetic variation in many species due to periodic climatic oscillations over the Pleistocene (Avise, 2000;Hewitt, 2000). ...
Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations' period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alectoris chukar in north and northwest China. A 1,152 - 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 - 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma)
... Oporornis tolmiei, (Mila et al. 2000), greenfinch, Carduelis chloris, (Merilä et al. 1997) and mountain sheep (Ramey II 1995). As in this study, Ramey II's (1995) study of mountain sheep in south-western North America found a lack of mitochondrial divergence among currently recognised subspecies. ...
... Phylogeographical structure has been documented in several avian species from Europe and North America (Merilä et al. 1997;Milá et al. 2007;Pitra et al. 2000;Barrowclough et al. 2004). Our analyses distinguished five lineages in Black Grouse with high posterior probability values for the divergence between northern and southern T. t. tetrix, T. t. mongolicus, T. t. ussuriensis and a western European clade. ...
The cold periods of the Pleistocene have had a striking impact on the diversification of most organisms in temperate regions. Phylogeographic patterns and postglacial expansion are poorly understood in the Black Grouse (Tetrao tetrix). This species is widely distributed across Eurasia, and has been divided into a number of subspecies on the basis of morphological differences and geographic isolation. To investigate the evolutionary history of the species, 143 samples from different regions were examined for a mtDNA control region fragment. Overall, analyses of mtDNA gave support for the divergence between Tetrao tetrix tetrix, T. t. ussuriensis and T. t. mongolicus. The analyses reveal the effects of colonisation out of glacial refugia on the genetic diversity and genetic structure of Black Grouse. The phylogeographical results are consistent with a demographic population expansion following a bell-shaped mismatch distribution, a star-shaped phylogeny and low nucleotide diversity. Patterns of postglacial dispersal imply that Black Grouse from southern Europe have been restricted to this area, and did not contribute to the genetic diversity of northern Europe. Instead, Black Grouse spread out to northern Europe from a refugium in the east and a possible one in western Europe, following the retreat of glacial ice sheets, although both refugia remain unidentified. We suggest that T. t. britannicus and T. t. viridanus correspond to northern T. t. tetrix, and that this lineage has diverged from the other subspecies. This division is tentative due to limited sampling, but it will facilitate the management of different evolutionary significant units of the species.
... Network analysis showed that DNA sequence of the haplotype of Large Beladi (LBB49) has the highest frequency and connected with the largest number forming a star-like structure. Such pattern of structure was found for different species of birds including Red winged Blackbird, Red poll finches, and Greenfinch [30,31]. The analysis also revealed convergent or reverse mutation among haplotypes LBB40, LBB56, and BTW1. ...
The objective of this study was to assess the genetic relationships and diversity and to estimate the amount of gene flow among the five chicken populations from Sudan and South Sudan and commercial strain of egg line White Leghorn chickens. The chicken populations were genotyped using mtDNA D-loop as a molecular marker. PCR product of the mtDNA D-loop segment was 600 bp and 14 haplotypes were identified. The neighbor-joining phylogenetic tree indicated that the indigenous Sudanese chickens can be grouped into two clades, IV and IIIa only. Median joining networks analysis showed that haplotype LBB49 has the highest frequency. The hierarchal analysis of molecular variance (AMOVA) showed that genetic variation within the population was 88.6% and the differentiation among the population was 11.4%. When the populations was redefined into two geographical zones, rich and poor Savanna, the results were fractioned into three genetic variations: between individuals within population 95.5%, between populations within the group 0.75%, and genetic variation between groups 3.75%. The pair wise F st showed high genetic difference between Betwil populations and the rest with F st ranging from 0.1492 to 0.2447. We found that there is large number of gene exchanges within the Sudanese indigenous chicken (Nm = 4.622).
... It is not possible to rule out H002 as a potential ancestral or co-ancestral haplotype, although it appears to be less widely distributed than H001. The overall haplotype distribution could be an indication of recent expansion of a population from one or a small number of founders (Ball et al. 1988, Merilä et al. 1997, Avise 2000. ...
... Q ST can be estimated from phenotypic distance P ST [66] using a measure of heritability (h 2 , proportion of additive genetic variance to phenotypic variance, V A /V P ) [66,67,68,69,70]. In wild populations, heritability h 2 is often unknown and needs to be estimated from largely comparable lab studies. ...
Studies comparing phenotypic variation with neutral genetic variation in modern humans have shown that genetic drift is a main factor of evolutionary diversification among populations. The genetic population history of our closest living relatives, the chimpanzees and bonobos, is now equally well documented, but phenotypic variation among these taxa remains relatively unexplored, and phenotype-genotype correlations are not yet documented. Also, while the adult phenotype is typically used as a reference, it remains to be investigated how phenotype-genotye correlations change during development. Here we address these questions by analyzing phenotypic evolutionary and developmental diversification in the species and subspecies of the genus Pan. Our analyses focus on the morphology of the femoral diaphysis, which represents a functionally constrained element of the locomotor system. Results show that during infancy phenotypic distances between taxa are largely congruent with non-coding (neutral) genotypic distances. Later during ontogeny, however, phenotypic distances deviate from genotypic distances, mainly as an effect of heterochronic shifts between taxon-specific developmental programs. Early phenotypic differences between Pan taxa are thus likely brought about by genetic drift while late differences reflect taxon-specific adaptations.
... In response to the Pleistocene ice ages, many organisms living in temperate regions experienced recurrent range shifts and population contractions (Hewitt 1996). In Europe, the concomitant recolonizations of northern regions can result in a latitudinal cline in populations' genetic variability (Merilä 1997). The greater mouse-eared bat (Myotis myotis), which is an endemic species restricted to the Western Palaearctic region, is prone to have followed such a scenario. ...
Keywords:Abudefduf;DNA markers microsatellite
... Geographic and climatic barriers present over such a broad area have been influential in creating morphological and molecular differences in many other species. For example, deserts of the southwestern United States and cyclic Pleistocene glacial episodes have served to diversify genetic histories in multiple vertebrate groups in northern latitudes (e.g., Hewitt 1996;Koepfli et al. 2007;Leaché and Mulcahy 2007;Lessa et al. 2003;Merilä et al. 1997;Sheffield and Thomas 1997;Zamudio and Greene 1997), whereas the Bolivar trough, or the deep-water trench dividing Central and South America until the completion of the w w w . m a m m a l o g y . ...
The long-tailed weasel (Mustela frenata) has the largest distribution of any mustelid in the Western Hemisphere, yet little is known of its genetic history. As a result of its broad distribution, the species provides an excellent model for identifying potential barriers influencing general phylogeographic patterns shared across multiple taxa. Here we used mitochondrial DNA with phylogenetic, phylogeographic, and molecular dating techniques to investigate molecular and geographical structure, as well as demographic history of M. frenata. Samples encompass 38 of the 42 recognized subspecies ranging from southern Canada to Bolivia. Our results suggest that long-tailed weasels are divided into distinct genetic clades, with eastern and western groups present in North America, 2 distinct lineages in Mexico and Central America separated by the trans-Mexican volcanic belt, and 1 clade in South America. Unlike other Mustela in North America, long-tailed weasels appear to have originated in the tropical areas of Mexico and Central America prior to dispersing 1st to the south before also expanding north in the Pleistocene.
... This is the highest number of lineages ever observed for a bird species in this region. Indeed, most phylogeographic studies performed on European birds resulted in the definition of only one to a maximum of three lineages, or no clear phylogeographic structure for the Western Palearctic (Merilä et al., 1997;Pitra et al., 2000;Liukkonen-Anttila et al., 2002;Pavlova et al., 2003;Randi et al., 2003;Zink et al., 2003;Kvist et al., 2004;Qu et al., 2005). One possible exception could be the tawny owl (Brito, 2005). ...
Cytochrome b gene sequence variation (902 bp) was used to investigate phylogenetic relationships and genetic differentiation among the four sub-species of European white-throated dipper Cinclus cinclus (Aves; Cinclidae). Six cytochrome b haplotypes were revealed, the most common one (H 13–4) was shared by all seven populations studied. Central Euro-pean C. c. aquaticus was genetically more diverse than the other subspecies (although not significantly so, due to small sample sizes), whereas our sample of the nominate subspecies from the French Pyrenees showed no haplotype variation. Pairwise comparisons of the four subspecies showed significant genetic differentiation between the taxa except for a lack of differentiation of C. c. hibernicus versus C. c. aquaticus and C. c. cinclus. The genetic structure and the phylogeographic pattern were not related to the geographic distribution of the four subspecies thus disputing the validity of the current infraspecific taxonomy of C. cinclus at least in Europe.
... The results obtained here suggest a similar process in A. australis and O. flavescens in a different timescale. Habitat contractions caused by Pleistocene glacial cycles across temperate regions have been proposed as a major process in reducing genetic diversity and shaping the current genetic structure in populations from the northern hemisphere (Rising & Avise 1993;Hewitt 1996;Merila¨et al. 1997;Zink 1997;Mila´et al. 2000). Other evidence came from studies of different species from the southern hemisphere, which include several species of plants (Allnutt et al. 1999(Allnutt et al. , 2003Premoli et al. 2002;Muellner et al. 2005) and fishes (Zattara & Premoli 2005;Ruzzante et al. 2006); the rock shag, S. magellanicus (Siegel-Causey 1997) and the saxicolous mouse, Phyllotis xanthopygus (Waterhouse, 1837) (Kim et al. 1998). ...
Analysing a 529 bp segment of the mitochondrial control region, we evaluated the role that Pleistocene glaciations may have had in shaping the genetic structure currently found in the two southernmost breedingareas of the South American fur seal, Arctocephalus australis. Additionally, we analysed if these two breedingareas correspond to different conservation units. We found 26 haplotypes in 54 individuals. Colonies from the Uruguayan breeding area did not show significant differences in haplotype frequencies, which suggest that they are remnants of a single ancient gene pool. The genealogical relationship between haplotypes revealed a pattern of phylogeographic structure with two main haplogroups corresponding to the different breeding areas. The analysis of molecular variance and the estimate of population divergence time also
indicated significant genetic differences and a long period of isolation between Atlantic and Pacific colonies, suggesting that these breeding areas would correspond to different conservation units.
... The BGL staff obtains both the mtDNA and microsatellite genotypes of all female red drum and the microsatellite genotypes of all male red drum held at SERF for potential use as broodstock. In red drum mtDNA maternity studies, which involved >1000 offspring and 14 broodstock mothers, BGL staff found no instances where the mtDNA genetic-tag sequences of the mothers and their offspring differed (unpublished data), nor do they expect to find any in the future, based on reported mutation rates for the mtDNA control region (Merilä et al., 1997). Thus, because of the unique mode of inheritance of mtDNA, the mtDNA genotypes of the broods are known if the mtDNA genotypes of the female broodstock are known. ...
... A common feature of many species showing little population structuring is that they inhabit recently deglaciated areas. The lack of population differentiation in these species may not imply extensive contemporary gene flow, but may instead reflect the impacts of relatively recent recolonization of deglaciated areas (Merilä et al. 1997). Although mtDNA data have been proven to be very useful in retrieving information on historical demography in bird species, they may lack the power to indicate the extent of contemporary gene flow. ...
The herring gull (Larus argentatus), which is one of the most abundant gulls in temperate North America, is used as an important bioindicator species, but little is known about its patterns of genetic variation. This study examines DNA sequence diversity in the cytochrome b gene of mitochondrial DNA (mtDNA) from herring gull colonies in the Great Lakes basin and from a site in the Maritimes. A 307-bp fragment of the gene was analyzed using a rapid mutation screening procedure coupling directed termination PCR (DT-PCR) with single-stranded conformation polymorphism (SSCP). Seven mtDNA haplotypes were revealed in 224 specimens with a common haplotype dominating all populations. Direct sequencing of a 1063-bp fragment of the cytochrome b gene identified 8 additional haplotypes, but the sequence divergence among all 15 haplotypes was very low (average 0.24%). These data suggest that herring gulls experienced a bottleneck during the last glaciation that is now reflected in their low levels of genetic divergence. The geographic distribution of mtDNA haplotypes indicates that gene flow among herring gull populations is sufficient to ensure genetic homogeneity in the Great Lakes, but insufficient to homogenize genetic variation between the Great Lakes and the Maritimes. Meanwhile, a comparison analysis of frozen egg specimens suggests a possible shift in the genetic composition of the Great Lakes populations over the last 15 years.
... The BGL staff obtains both the mtDNA and microsatellite genotypes of all female red drum and the microsatellite genotypes of all male red drum held at SERF for potential use as broodstock. In red drum mtDNA maternity studies, which involved >1000 offspring and 14 broodstock mothers, BGL staff found no instances where the mtDNA genetic-tag sequences of the mothers and their offspring differed (unpublished data), nor do they expect to find any in the future, based on reported mutation rates for the mtDNA control region (Merilä et al., 1997). Thus, because of the unique mode of inheritance of mtDNA, the mtDNA genotypes of the broods are known if the mtDNA genotypes of the female broodstock are known. ...
Abstract Stock enhancement, the supplementation of depleted wild fish and invertebrate stocks with individuals reared in aquaculture facilities orcaptured from other populations, is becoming an increasingly popular method ,of bolstering heavily fished populations. Although many ,different aspects of marine ,stock enhancement ,have ,been ,evaluated for several species of fish ,and invertebrates, a multidisciplinary approach is often not feasible for many programs. In addition, a systematic, coordinated, comprehensive, monitoring program is not commonly used to test whether stock enhancement ,efforts actually result in measurable ,increases in fishery output. In 1999, the Florida Marine Research Institute in St. Petersburg, Florida, and Mote Marine Laboratory in Sarasota, Florida, initiated a multiyear stock enhancement experiment to supplement the red drum (Sciaenops ocellatus) population in Tampa Bay, Florida, USA. The original experimental,design for releasing aquacultured (hatchery-reared) red drum ,into Tampa ,Bay included the following variables: two riverine systems, several sections within each system, two
... e pattern in which one very common haplotype, presumably ancestral, lies at the centre of a network and is connected by independent mutation steps to many much rarer haplotypes, is usually regarded as indicative of a population having recently expanded in size from one or a small number of founders (Avise 2000; see examples in Ball et al . 1988 andMerilä et al . 1997). Subnetworks I and III conform rather well to this description. Subnetwork II includes two central haplotypes (34 and 35) also each connected to many other haplotypes. In those cases, however, the central haplotypes are only slightly more common than some of the tip haplotypes. Some of the peripheral haplotypes are even more frequent th ...
The pattern of genetic variation in the leaf beetle Gonioctena pallida was investigated inside the Vosges mountains using a highly variable 363 bp DNA fragment of the mitochondrial control region. Sequencing of 242 individuals, sampled in a geographical area of 100 × 40 km, identified 61 haplotypes whose genealogy was inferred. The resulting haplotype network exhibits four star-like phylogenies, two of which may be indicative of a population having recently expanded in size from a small number of founders. Nested clade analysis suggested multiple past expansion events, but also isolation by distance and possibly past fragmentation events, as the causes of the detected geographical associations of haplotypes. These results indicate the existence of effective barriers to gene flow inside the investigated area. Because the oldest demographic events inferred in the nested clade analysis were identified as expansion events, we hypothesize that a small population of founders have expanded not only in size, but also in geographical range from the south towards the north and east of the Vosges.
We compared sequences from two mitochondrial DNA (mtDNA) genes (ND2, ND3) in Savannah Sparrows (Passerculus sandwichensis; n = 112) sampled from Baja California (five sites), coastal Sonora and the continental range (eight sites). Populations from Baja California, San Diego and Sonora formed a clade within which there was no phylogeographic structure; this clade merits species status (Passerculus rostratus). The other clade, consisting of phenotypically “typical” savannah sparrows, should be classified as P. sandwichensis. Among the typical sparrows, there was no phylogeographic structure, although two major clades were discovered. Representatives of each of the two main clades occurred at most sampling localities, excluding Suisan Bay, California and Sable Island, Nova Scotia, Canada. Haplotypes found on Sable Island, representing the “Ipswich Sparrow,” were not distinctive, thereby failing to support species status for this taxon. On Isla San Benito, a single haplotype was found, which also occurred in other Mexican localities. The results for Sable Island and Isla San Benito show that size and plumage coloration can evolve rapidly.
Variación en ADN Mitocondrial, Límites entre Especies y Evolución Rápida de la Coloración del Plumaje y el Tamaño en Passerculus sandwichensis
Resumen. En este estudio comparamos secuencias de dos genes mitocondriales (ND2 y ND3) entre individuos de la especie Passerculus sandwichensis (n = 112) muestreados en Baja California (5 sitios), la costa de Sonora y el rango de distribución continental (8 sitios). Las poblaciones de Baja California, San Diego y Sonora formaron un clado, al interior del cual no existió estructura filogeográfica; este clado merece estatus de especie (Passerculus rostratus). El otro clado, conformado por individuos fenotípicamente “típicos”, debe clasificarse como P. sandwichensis. Entre los individuos típicos no existió estructura filogeográfica, aunque se descubrieron dos clados principales. Individuos representativos de cada uno de estos dos clados se encontraron en la mayoría de las localidades, excepto Suisan Bay, California y Sable Island, Nova Scotia. Los haplotipos encontrados en Sable Island, correspondientes al “gorrión de Ipswich” no fueron distintivos, lo que no apoya el estatus de especie para este taxón. En Isla San Benito se encontró un solo halpotipo, el cual también se encontraba en otras localidades mexicanas. Los resultados de Sable Island e Isla San Benito muestran que el tamaño y la coloración del plumaje pueden evolucionar rápidamente.
During the Pleistocene, the habitat of the noctule bat (Nyctalus noctula) was limited to small refuge areas located in Southern Europe, whereas the species is now widespread across this continent. Using mtDNA (control region and ND1 gene) polymorphisms, we asked whether this recolonization occurred through bottlenecks and whether it was accompanied by population growth. Sequences of the second hypervariable domain of the control region were obtained from 364 noctule bats representing 18 colonies sampled across Europe. This yielded 108 haplotypes that were depicted on a minimum spanning tree that showed a starlike structure with two long branches. Additional sequences obtained from the ND1 gene confirmed that the different parts of the MST correspond to three clades which diverged before the Last Glacial Maximum (18,000 yrC(14) BP), leading to the conclusion that the noctule bat survived in several isolated refugia. Partitioning populations into coherent geographical groups divided our samples (φCT = 0.17; P = 0.01) into a group of highly variable nursing colonies from central and eastern Europe and less variable, isolated colonies from western and southern Europe. Demographic analyses suggest that populations of the former group underwent demographic expansions either after the Younger Dryas (11,000-10,000 yrC(14) BP), assuming a fast mutation rate for HV II, or during the Pleistocene, assuming a conventional mutation rate. We discuss the fact that the high genetic variability (h = 0.69-0.96; π = 0.006-0.013) observed in nursing colonies that are located some distance from potential Pleistocene refugia is probably due to the combined effect of rapid evolution of the control region in growing populations and a range shift of noctule populations parallel to the recovery of forests in Europe after the last glaciations.
The chukar partridge (Alectoris chukar) is distributed in north and northwest of China, in mountainous areas that were heavily affected by cyclic climate and landscape changes during the last Pleistocene glaciations. Some partridge populations have colonized and expanded their present ranges only after deglaciation and recent deforestation by human. Consequently, partridges from different areas could be genetically differentiated. In this study, a 1152–1154 bp portion of the mitochondrial DNA control region were analyzed for all 279 specimens collected from 28 populations through their distribution in China. A total number of 91 haplotypes were defined by 113 variable sites. The mean haplotype diversity and nucleotide diversity were 0.939 ± 0.008 and 0.0030 ± 0.0017, respectively, for chukar. Haplotype diversity among the 28 populations varied from 0.600 ± 0.215 (HH) to 1.000 ± 0.272 (SBC), and nucleotide diversity ranged from 0.0006 ± 0.0007 (HJ) to (0.0071 ± 0.0041) (HEG). The nucleotide diversity of chukar was descending from west to east and a possible historical scenario might be that A. chukar inhabited central Asia, and then dispersed eastward. Phylogenetic analyses indicated that there was no distinct phylogeographic structure in chukar populations in China. Haplotype network of chukar was star-like with some common haplotypes shared by different samples came from different populations as center. Both unstructured phylogeographic tree and star-like haplotype network are signatures of population expansion.
In order to understand the phylogeographic structure of Pheropsophus jessoensis Morawitz in the Tsinling Mountains, a fragment with 789 bp from the mtCoI gene was sequenced for the 184 P. jessoensis individuals from 25 geographical populations belonging to two geographic areas. A total of 55 polymorphic sites were found, and 67 haplotypes were identified. The haplotype diversity was high (Hd = 0.9550), while the nucleotide diversity was relatively low (Pi = 0.0049). The Kimura 2-parameter (K2P) genetic distance of the P. jessoensis between west Tsinling population and east Tsinling population or among the 25 populations was small, with the values ranged from 0.0026 to 0.0072. The analysis of molecular variance (AMOVA) and the nested clade phylogeographical analysis (NCPA) revealed the significant genetic subdivision among the individuals within populations, but there existed no remarkable phylogeographic structure between the eastern part and the western part of Tsinling Mountains. The NCPA showed certain geographical association of haplotypes. The results from mismatch distribution and neutrality tests suggested that the present complex genetic pattern of P. jessoensis in Tsinling Mountains was resulted from the restricted gene flow with isolation by distance, and from the sudden or contiguous range expansion. The demographic history analysis revealed that this species could have experienced a relatively recent population expansion occurring in the later Pleistocene (0.05-0.23 Ma). The climatic oscillations during this period might have affected the geographical isolation and genetic differentiation of P. jessoensis in this area.
Die Verwendung von unbestimmten Rechtsbegriffen bereitet Schwierigkeiten bei der Anwendung und gefährdet die Rechtssicherheit. In vielen Rechtsnormen des Umweltrechts (u. a. UVPG) findet der unbestimmte Rechtsbegriff „voraussichtliche erhebliche Umweltauswirkungen" Verwendung. In dieser Arbeit wird ein Beitrag zur Konkretisierung dieses Begriffes im Rahmen der strategischen Umweltprüfung (SUP) geleistet. Dabei wird ein interdisziplinärer Forschungsansatz gewählt, der durch juristische, wie naturwissenschaftliche Methodik geprägt ist und dazu beiträgt das Schutzgut der Biodiversität genauer zu bestimmen. rnDazu wird zunächst auf juristischer Ebene geprüft, ob aus dem UVPG sowie weiteren Rechtsnormen des Umweltrechts Informationen zur Konkretisierung dieses Begriffes zu gewinnen sind. Hiernach ergibt sich, dass der Erheblichkeitsbegriff insbesondere dazu dient, Bagatellfälle auszuklammern und Angleichungen zwischen den Rechtsnormen zu erreichen. Da die SUP seit 2005 geltendes Recht ist, ist es wichtig zu sehen, wie in der Gutachtenpraxis mit diesem unbestimmten Rechtsbegriff umgegangen wird. Daher sind vier Umweltberichte gemäß §14g Satz 2 Nr.5 UVPG überprüft worden. Es stellte sich heraus, dass die Umweltberichte weder in der Lage sind die voraussichtlichen erheblichen Umweltauswirkungen zu Konkretisieren, noch wie es vom UVPG gemäß §14g Satz 2 Nr.3 UVPG gefordert wird das Schutzgut der Biodiversität hinreichend darzustellen. rnAus naturwissenschaftlicher Sicht wurden zunächst natürliche und anthropogene Auswirkungen auf die Biodiversität geprüft, um so die Faktoren zu ermitteln, die die Biodiversität besonders negativ zu beeinflussen vermögen. Demnach gilt es die Faktoren Habitatfragmentierung, Angleichungsprozesse (Biotic homogenization) und Intensität der Landnutzung im Rahmen der SUP frühzeitig zu vermeiden. Die „Convention of Biodiversity“ zählt neben den Arten und Landschaften auch die genetische Ebene zum Begriff der Biodiversität. So ist es sinnvoll auch genetische Aspekte in die Schadensbewertung zu integrieren. Daher wurden in einer phylogeographischen Analyse die zwei Genorte Cytochrom Oxidase I und die Control Region der mtDNA des silbergrünen Bläuling, Polyommatus coridon (30 Populationen) untersucht. Es konnte gezeigt werden, dass genetische Analysen zwar wichtige Informationen für die Konkretisierung des unbestimmten Rechtsbegriffes liefern, aber dennoch mit Vorsicht diesbezüglich zu behandeln sind. rnLetztendlich stellte sich heraus, dass die Konkretisierung des unbestimmten Rechtbegriffes der voraussichtlichen erheblichen Umweltauswirkungen sich im Rahmen der strategischen Umweltprüfung mehr als schwierig und in Hinblick auf der Konzeption der SUP wenig sinnvoll erweist. rn
Study about stopover ecology of small migrants in Salburua park (northern Iberia)
Common Crossbill subspecies have been described according to morphological traits, vocalizations and geographical distribution. In this study, we have tried to determine whether the subspecies correspond to clear-cut mitochondrial DNA lineages, by sequencing 717 bp of the control region from individuals taken at several sampling locations in North America and the Western Palaearctic. We find 22 haplotypes from the 37 sampled individuals with a mean divergence of 0.0118 0.0069 (mean SD). We find a mixing of the mitochondrial haplotypes at the continental level among the different types or subspecies previously described. Morphological differentiation (in bill size and shape essentially) shows the possibility of rapid local adaptation to fluctuating resources (coniferous seeds), without necessarily promoting the development of reproductive barriers between morphs.
A portion of the mitochondrial control region (494 bp) was sequenced in 106 great reed warblers sampled in six breeding populations in Europe and one wintering population in Africa. In total, 33 different haplotypes were found. There was little evidence of divergence between populations in northern and western Europe whereas the sample from Greece differed significantly from the other European breeding populations. The lowest haplotype diversity was found near the distribution range limit in Sweden and in The Netherlands suggesting recent effects of bottlenecks/founder events in these areas. A neighbour-joining analysis of the different haplotypes placed the haplotypes into two distinctive clades, A and B. The divergence of the two clades was on average 1.29%. Accounting for the within clade variation suggested a divergence time between these lines approximately 70 000 years BP. The frequency of the two clades changed longitudinally across Europe with the A haplotype in the west and the B haplotype in the east. All birds from Kenya carried the B haplotype suggesting an origin of these birds east of Latvia/Greece. The long-term female effective population size was estimated to be 20 000 individuals, which is approximately 2% of current population size.
The glacial refugium hypothesis (GRH) proposes that glaciers promoted differentiation and generation of intraspecific diversity by isolating populations in ice-free refugia. We tested three predictions of this hypothesis for the evolutionary divergence of rock ptarmigan (Lagopus mutus) during the Wisconsin glaciation of the late Pleistocene. To do this, we examined subspecies distributions, population genetic structure, and phylogenetic relationships in 26 populations across North America and the Bering Sea region. First, we analyzed sequence variation in the mitochondrial control region, in a nuclear intron (Gapdh), and in an internal transcribed spacer (ITS1). Control region sequences of 154 rock ptarmigan revealed strong population and phylogeographic structure. Variation in intron sequences of 114 rock ptarmigan also revealed significant population structure compatible with results for the control region. Rock ptarmigan were invariant for ITS1. Second, we show that five known Nearctic refugia and an Icelandic refugium are concordant with the current distribution of morphologically distinct subspecies; five of these six refugia are geographically concordant with the distribution of closely related control region haplotypes. Third, our estimates of the time since phylogenetic lineages diverged predated the last glacial maximum for all but two lineages. In addition, all lines of evidence suggest that two unknown refugia in the Bering Sea region supported rock ptarmigan during the Wisconsin glaciation. Overall, our results are most consistent with the hypothesis that isolated populations of rock ptarmigan diverged in multiple refugia during the Wisconsin and that geographic variation reflects patterns of recolonization of the Nearctic after the ice receded. The GRH may therefore offer the most plausible explanation for similar biogeographic patterns in a variety of Nearctic vertebrates.
The geographic pattern of mtDNA variation in lemmings from 13 localities throughout the Eurasian Arctic was studied by using eight restriction enzymes and sequencing of the cytochromebregion. These data are used to reveal the vicariant history ofLemmus, and to examine the effect of the last glaciation on mtDNA variation by comparing diversity in formerly glaciated areas to the diversity in non-glaciated areas. Phylogenetic congruence across different Arctic taxa and association between observed discontinuities, and probable Pleistocene barriers, suggest that glacial-interglacial periods were crucial in the vicariant history ofLemmus. Differences in amount of divergence (2.1–9.1%) across different historical barriers indicate chronologically separate vicariant events during the Quaternary. Populations from a formerly glaciated area are no less variable than those in the non-glaciated area. Regardless of glaciation history, no population structure and high haplotype diversity were found within geographic regions. The lack of population structure indicates that populations with high ancestral haplotype diversity shifted their distribution during the Holocene, and that lemmings tracked a changing environment during the Quaternary without reduction of effective population size.
Australian magpies (Gymnorhina tibicen) are group-living birds found across much of mainland Australia. Adults commonly remain in a breeding territory until death. Young of the year either remain on the natal (birth) site or are forced by their parents to disperse. Observational studies in south-eastern Australia suggest that most dispersing juveniles settle within 7 km of their natal territory. Therefore, despite potential for considerable gene flow (via flight), social organization predisposes magpies towards local population structuring. In this study, we measured genetic variation at both nuclear (allozyme) and mitochondrial loci and found evidence of substantial gene flow over very large distances (up to 1599 km). Thus, some juvenile magpies may disperse much greater distances than was previously thought. For mtDNA, geographic and genetic distance were strongly correlated, consistent with a pattern of isolation by distance. Therefore, although female gene flow is substantial it is apparently geographically restricted over large distances, in approximately a stepping-stone fashion. We conclude that a strong relationship between gene flow and geographic distance can develop even over large distances if populations have experienced no major historical disturbances to gene flow.
Bats are being increasingly recognized as reservoir hosts of highly pathogenic and zoonotic emerging viruses (Marburg virus, Nipah virus, Hendra virus, Rabies virus, and coronaviruses). While numerous studies have focused on the mentioned highly human-pathogenic bat viruses in tropical regions, little is known on similar human-pathogenic viruses that may be present in European bats. Although novel viruses are being detected, their zoonotic potential remains unclear unless further studies are conducted. At present, it is assumed that the risk posed by bats to the general public is rather low. In this review, selected viruses detected and isolated in Europe are discussed from our point of view in regard to their human-pathogenic potential. All European bat species and their roosts are legally protected and some European species are even endangered. Nevertheless, the increasing public fear of bats and their viruses is an obstacle to their protection. Educating the public regarding bat lyssaviruses might result in reduced threats to both the public and the bats.
The geographic pattern of mtDNA variation in lemmings from 13 localities throughout the Eurasian Arctic was studied by using eight restriction enzymes and sequencing of the cytochrome b region. These data are used to reveal the vicariant history of Lemmus, and to examine the effect of the last glaciation on mtDNA variation by comparing diversity in formerly glaciated areas to the diversity in non‐glaciated areas. Phylogenetic congruence across different Arctic taxa and association between observed discontinuities, and probable Pleistocene barriers, suggest that glacial‐interglacial periods were crucial in the vicariant history of Lemmus. Differences in amount of divergence (2.1–9.1%) across different historical barriers indicate chronologically separate vicariant events during the Quaternary. Populations from a formerly glaciated area are no less variable than those in the non‐glaciated area. Regardless of glaciation history, no population structure and high haplotype diversity were found within geographic regions. The lack of population structure indicates that populations with high ancestral haplotype diversity shifted their distribution during the Holocene, and that lemmings tracked a changing environment during the Quaternary without reduction of effective population size.
Contemporary DNA sequences can provide information about the historical demography of a species. However, different molecular markers are informative under different circumstances. In particular, mitochondrial (mt)DNA is uniparentally inherited and haploid in most vertebrates and thus has a smaller effective population size than diploid, biparentally inherited nuclear (n)DNA. Here, we review the characteristics of mtDNA and nDNA in the context of historical demography. In particular, we address how their contrasting rates of evolution and sex-biased dispersal can lead to different demographic inferences. We do so in the context of an extensive review of the vertebrate literature that describes the use of mtDNA and nDNA sequence data in demographic reconstruction. We discuss the effects of coalescence, effective population size, substitution rates, and sex-biased dispersal on informative timeframes and expected patterns of genetic differentiation. We argue that mtDNA variationin species with male-biased dispersal can imply deviations from neutrality that do not reflect actual population expansion or selection. By contrast, mtDNA can be more informative when coalescence has occurred within the recent past, which appears to be the case with many vertebrates. We also compare the application and interpretation of demographic and neutrality test statistics in historical demography studies. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, ●●, ●●–●●.
In 2001-2005 we sampled permanently marked big brown bats (Eptesicus fuscus) at summer roosts in buildings at Fort Collins, Colorado, for rabies virus neutralizing antibodies (RVNA). Seroprevalence was higher in adult females (17.9%, n = 2,332) than males (9.4%, n = 128; P = 0.007) or volant juveniles (10.2%, n = 738; P<0.0001). Seroprevalence was lowest in a drought year with local insecticide use and highest in the year with normal conditions, suggesting that environmental stress may suppress RVNA production in big brown bats. Seroprevalence also increased with age of bat, and varied from 6.2 to 26.7% among adult females at five roosts sampled each year for five years. Seroprevalence of adult females at 17 other roosts sampled for 1 to 4 years ranged from 0.0 to 47.1%. Using logistic regression, the only ranking model in our candidate set of explanatory variables for serological status at first sampling included year, day of season, and a year by day of season interaction that varied with relative drought conditions. The presence or absence of antibodies in individual bats showed temporal variability. Year alone provided the best model to explain the likelihood of adult female bats showing a transition to seronegative from a previously seropositive state. Day of the season was the only competitive model to explain the likelihood of a transition from seronegative to seropositive, which increased as the season progressed. We found no rabies viral RNA in oropharyngeal secretions of 261 seropositive bats or in organs of 13 euthanized seropositive bats. Survival of seropositive and seronegative bats did not differ. The presence of RVNA in serum of bats should not be interpreted as evidence for ongoing rabies infection.
The studies of uplift and glaciations of the Tibetan Plateau are summarized, and a series of recent case studies of the endemic species based on DNA sequences are detailed. In general, these molecular data show that all the organisms originated from Early Pliocene to Late Miocene, and then multi-stages of divergence/speciation occurred within each taxa following their original occupation on the plateau, mainly as a result of periodic glacial cycles and geographic isolation. The regional fauna may have undergone several range contractions and expansions during the Pleistocene glaciations. However, the population expansion and refugia may vary in space, time, and extent. The regional fauna of the Tibetan Plateau may be combinations of ancient movement from adjacent zoogeographical regions, speciation in situ, and postglacial colonization from adjacent areas. Geomorphic and climatic changes on the plateau definitely have a remarkable influence on the regional and adjacent biogeographic patterns, and the mechanism is very complex.
Geographical variation in two related seabird species, the razorbill (Alca torda) and common guillemot (Uria aalge), was investigated using sequence analysis of mitochondrial DNA (mtDNA) control regions. We determined the nucleotide sequence of the variable 5′ segment of the control region in razorbills and common guillemots from breeding colonies across the Atlantic Ocean. The ecology and life history characteristics of razorbill and common guillemot are in many respects similar. They are both considered highly philopatric and have largely overlapping distributions in temperate and subarctic regions of the North Atlantic, yet the species were found to differ widely in the extent and spatial distribution of mtDNA variation. Moreover, the differences in genetic differentiation and diversity were in the opposite direction to that expected from a consideration of traditional classifications and current population sizes. Indices of genetic diversity were highest in razorbill and varied among colonies, as did genotype frequencies, suggestive of restrictions to gene flow. The distribution of genetic variation suggests that razorbills originated from a refugial population in the south-western Atlantic Ocean through sequential founder events and subsequent expansion in the east and north. In common guillemots, genetic diversity was low and there was a lack of geographical structure, consistent with a recent population bottleneck, expansion and gene flow. We suggest that the reduced level of genetic diversity and differentiation in the common guillemot is caused by an inherent propensity for repeated population bottlenecks and concomitantly unstable population structure related to their specialized feeding ecology.
Although comparisons of variation patterns with theoretical expectations and across species are playing an increasingly important role in systematics, there has been a lack of appropriate procedures for statistically testing the proposed hypotheses. We present a series of statistical tests for hypotheses of morphological integration and for interspecific comparison, along with examples of their application. These tests are based on various randomization and resampling procedures, such as Mantel's test with its recent extensions and bootstrapping. They have the advantage of avoiding the specific and strict distributional assumptions invoked by analytically-based statistics. The statistical procedures described include one for testing the fit of observed correlation matrices to hypotheses of morphological integration and a related test for significant differences in the fit of two alternative hypotheses of morphological integration to the observed correlation structure. Tests for significant similarity in the patterns and magnitudes of variance and correlation among species are also provided.
Genetic and morphological attributes of modern Pinus contorta spp latifolia (Rocky Mountain subspecies) are related to time since founding. Reduced allelic diversity towards the northern periphery may result simply from the stochastic effects of repeated long-distance founding events during continental-scale, postglacial spread. An increase in the ability of seeds to disperse as migration proceeds may result from directional selection associated with long-distance dispersal events occurring as part of the migration process. The magnitude of differences between central and marginal populations would be smaller because gene flow between populations increases as distance between populations decreases. -from Authors
Breeding redpoll finches (Aves: Carduelinae) show extensive plumage and size variability and, in many cases, a plumage polymorphism that is not related to age or sex. This has been ascribed to extreme phenotypic variation within a single taxon or to moderate variability within distinct taxa coupled with hybridization. The predominant view favors the recognition of two largely sympatric species: Carduelis flammea, comprised of four well marked subspecies-flammea, cabaret, islandica, and rostrata; and C. hornemanni, comprised of two subspecies-hornemmani and exilipes. We studied representative samples of these putative subspecies (except islandica) for variation in mitochondrial DNA (mtDNA). Using 20 informative restriction enzymes that recognized 124 sites (642 base pairs [bp] of sequence or approximate to 3.7% of the molecule), we identified 17 RFLP haplotypes in the 31 individuals surveyed. The haplotypes formed a simple phylogenetic network with most clones diverging by a single site difference from a common haplotype found in almost half of the individuals. Within populations and taxa, levels of mtDNA diversity were similar to those observed in other avian species. The pattern of mtDNA divergence among populations was statistically unrelated to their geographic or traditional taxonomic relationships, and the estimated distance between the two traditionally recognized species was very small relative to those typically observed among avian sister species. Redpolls are highly vagile and have very large effective population sizes that may be relatively stable over the long term. Under these conditions, an absence of mtDNA differentiation between reproductively isolated, but recently diverged, taxa is not necessarily surprising. Hybridization between imperfectly isolated taxa might also have impeded mtDNA differentiation or contributed to its loss. Other explanations for the conflicting patterns of genetic homogeneity and phenotypic polymorphism in redpolls include models of genetic polymorphism at a major locus having broad pleiotropic or epistatic effects, and various ecophenotypic models (e.g., niche polymorphism, threshold response mechanisms, phenotypic modulation, developmental conversion). Distinguishing among these possibilities will require detailed knowledge of the genetic or ecophenotypic basis of phenotypic variation in redpolls.
Concerns genetic variability in the nominate subspecies, O. d. dalli, from 3 parts of its N Alaskan distribution: the Alaskan Range, the Tanana Hills and the Brooks Range. These areas are 150-200 km apart. Their populations have been isolated from each other since the end of the Wisconsinan glaciation. -from Authors
Discusses mitochondrial DNA (mtDNA) sequences as important source of data about the history of human species. journal article
The predominant role of Eptesicus serotinus in the epizootic of bat rabies in Europe was further outlined by the first isolation of the rabies virus from this species in France. The distribution of the virus was studied in naturally infected E. serotinus bats at the time of death and suggested that the papillae of the tongue and the respiratory mucosa may play a role in virus production and excretion. The analysis of 501 French rabies virus isolates from various animal species by antinucleocapsid monoclonal antibodies indicated that transmission of the disease from bats to terrestrial animals is unlikely. The antigenic profile of two isolates from French bats corresponded to that of European bat lyssavirus type 1 (EBL1). Comparisons of 12 different isolates from bats with antinucleocapsid and antiglycoprotein monoclonal antibodies and by direct sequencing of the polymerase chain reaction amplification product of the N gene indicated that EBL1, EBL2, Duvenhage virus (serotype 4 of lyssavirus), and the European fox rabies virus (serotype 1) are phylogenetically distant. They formed four tight genetic clusters named genotypes. EBL1 was shown to be antigenically and genetically more closely related to Duvenhage virus than to EBL2. We propose that EBL1 and EBL2 constitute two distinct genotypes which further serologic characterization will probably classify as new serotypes. We also report a simple method for the rapid characterization of EBL based on the digestion of the polymerase chain reaction product of the N gene by three restriction endonucleases.
We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.
The understanding of the genetic structure of a species can be improved by considering together data from different types of genetic markers. In the past, a number of worldwide populations of Drosophila melanogaster have been extensively studied for several such markers, including allozymes, chromosomal inversions, and quantitative characters. Here we present results from a study of restriction-fragment-length polymorphisms of mitochondrial DNA (mtDNA) in 92 isofemale lines from many of the same geographic populations of D. melanogaster. Eleven restriction enzymes were used, of which four revealed restriction-site polymorphism. A total of 24 different haplotypes were observed, of which 18 were unique to single populations. In many populations, the unique haplotypes have reached high frequency without being observed in neighboring populations. A Wagner parsimony tree reveals that mutationally close variants show geographical clumping, suggesting local differentiation of mtDNA in populations. The Old-World and the New-World populations are differentiated, with the predominant Old-World haplotype being virtually absent from the New World. These results contrast with those for the nuclear genes, in which many loci show parallel clines in different continents, and suggest a common origin of D. melanogaster populations in North America.
Restriction endonuclease analysis of mtDNA was used to examine the genetic relatedness of several geographically separated isolines of the Drosophila mercatorum subgroup. In addition, we examined the temporal and spatial distribution of two mtDNA restriction site polymorphisms produced by the enzymes BstEII and BstNI at a single locality--Kamuela, Hawaii. Due to small sample sizes of some collections and the undesirable dependance of the estimation of polymorphism frequency on its variance, an arcsin square root transformation of the frequency data was used. We also use an Fst estimator of our transformed frequencies to demonstrate considerable spatial and temporal differentiation within the Kamuela population. In contrast, isozyme data from the same population reveals no pattern of differentiation. The temporal and geographic heterogeneity and population subdivision detected with mtDNA analysis also is consistent with the known dispersal behavior and ecological constraints of this species. The mtDNA data in conjunction with the isozyme data show that the population structure of the Kamuela D. mercatorum is close to the boundary line separating panmixia from subdivision, a conclusion that could not be made from isozyme data alone.
A total of 1,745, 362, and 536 bats collected in Alberta, British Columbia, and Saskatchewan, respectively, was tested for rabies virus between 1979 and 1983. Only one (0.1%) of 769 bats collected at random from buildings was infected with rabies virus in contrast to 95 (5%) of 1,874 symptomatic, rabies-suspect bats submitted for testing. The pattern of infection in the rabies-suspect bats was similar in Alberta and Saskatchewan, but differed in British Columbia. Rabies was diagnosed in four species of bats in each of Alberta and Saskatchewan, but in seven species in British Columbia. Annual prevalence in rabies-suspect bats was similar in colonial species within each province. Rabies was found rarely in suspect little brown bats (Myotis lucifugus) (less than 1%). In suspect big brown bats (Eptesicus fuscus), the prevalence was low in Saskatchewan (3%), moderate in Alberta (10%), and high in British Columbia (25%). Big brown bats accounted for over 55% of the rabid bats detected in each province. Annual prevalence reported in silver-haired bats (Lasionycteris noctivagans) and hoary bats (Lasiurus cinereus) was variable in all three provinces. Rabies is enzootic in northern insectivorous bats.
Hypervariable segments of the control region of mtDNA as well as part of the cytochrome b gene of Dunlins were amplified with PCR and sequenced directly. The 910 base pairs (bp) obtained for each of 73 individuals complete another of the few sequencing studies that examine the global range of a vertebrate species. A total of 35 types of mtDNA were detected, 33 of which were defined by the hypervariable-control-region segments. Thirty of the latter were specific to populations of different geographic origin in the circumpolar breeding range of the species. The remaining three types indicate dispersal between populations in southern Norway and Siberia, but female-mediated flow of mtDNA apparently is too low to overcome the effects of high mutation rates of the control-region sequences, as well as population subdivision associated with historical range disjunctions. A genealogical tree relating the types grouped them into five populations: Alaska, West Coast of North America, Gulf of Mexico, western Europe, and the Taymyr Peninsula. The Dunlin is thus highly structured geographically, with measures of mutational divergence approaching 1.0 for fixation of alternative types in different populations. High diversity of types within populations as well as moderate long-term effective population sizes argue against severe population bottlenecks in promoting this differentiation. Instead, population fragmentation in Pleistocene refuges is the most plausible mechanism of mtDNA differentiation but at a much earlier time scale than suggested previously with morphometric data.
To determine the prevalence of European Bat Lyssavirus 1 (EBL1), antibodies plasma samples were obtained from 175 serotine bats (Eptesicus serotinus) from four colonies in southern Spain between September of 1991 and September 1992. Five bats were detected with EBL1 virus in one colony in 1989. The prevalence of antibodies rose to 74% in one of the colonies studied (Villarrasa) in the spring of 1992. After a few months the prevalence declined to under 10%. Individuals with a high antibody level in the spring (up to ED50 = 280) had very low titers or no antibodies in the following summer and autumn.
Existing methods for analyzing nucleotide diversity require investigators to identify relevant hierarchical levels before beginning the analysis. We describe a method that partitions diversity into hierarchical components while allowing any structure present in the data to emerge naturally. We present an unbiased version of NEI's nucleotide diversity statistics and show that our modification has the same properties as WRIGHT's FST. We compare its statistical properties with several other FST estimators, and we describe how to use these statistics to produce a rooted tree of relationships among the sampled populations in which the mean time to coalescence of haplotypes drawn from populations belonging to the same node is smaller than the mean time to coalescence of haplotypes drawn from populations belonging to different nodes. We illustrate the method by applying it to data from a recent survey of restriction site variation in the chloroplast genome of Coreopsis grandiflora.
Episodes of population growth and decline leave characteristic signatures in the distribution of nucleotide (or restriction) site differences between pairs of individuals. These signatures appear in histograms showing the relative frequencies of pairs of individuals who differ by i sites, where i = 0, 1, .... In this distribution an episode of growth generates a wave that travels to the right, traversing 1 unit of the horizontal axis in each 1/2u generations, where u is the mutation rate. The smaller the initial population, the steeper will be the leading face of the wave. The larger the increase in population size, the smaller will be the distribution's vertical intercept. The implications of continued exponential growth are indistinguishable from those of a sudden burst of population growth Bottlenecks in population size also generate waves similar to those produced by a sudden expansion, but with elevated uppertail probabilities. Reductions in population size initially generate L-shaped distributions with high probability of identity, but these converge rapidly to a new equilibrium. In equilibrium populations the theoretical curves are free of waves. However, computer simulations of such populations generate empirical distributions with many peaks and little resemblance to the theory. On the other hand, agreement is better in the transient (nonequilibrium) case, where simulated empirical distributions typically exhibit waves very similar to those predicted by theory. Thus, waves in empirical distributions may be rich in information about the history of population dynamics.
Although papers concerned with electrophoresis and systematics have been appearing in the ornithological literature since the early 1950s (see review in Sibley et al., 1974), a period of rapid development of biochemical techniques and methods of analysis began only in the middle 1960s when empirical and theoretical population geneticists devoted increasing attention to the field. These workers were concerned not with questions of systematics, but rather with problems of the nature of evolutionary processes (Lewontin, 1974). Ornithologists did not adopt these new techniques and analyses as quickly as other evolutionary biologists; the first quantitative studies of individual heterozygosity and genetic differentiation in natural populations of birds did not appear until the late 1970s (see, for example, Smith and Zimmerman, 1976; Barrowclough and Corbin, 1978).
We surveyed mtDNA restriction-site variation in song sparrows taken from across their continental range. Despite marked geographic variation in size and plumage color, mtDNA variation was not geographically structured. Subspecies were not identifiable by mtDNA analysis. We suggest that postglaciation dispersal scattered mtDNA haplotypes across the continent, explaining the lack of mtDNA geographic patterns. Evolution of size and plumage coloration has probably proceeded faster than mtDNA evolution, leading to the well-structured continental pattern of morphological variation. We suggest that the nonordered geographic distribution of haplotypes reflects the recency of population establishment following completion of range expansion. Dispersal distance was estimated from the mtDNA data at 6.1 km per generation, an order of magnitude greater than that (0.3 km) estimated from demographic data. Island samples were not especially different from continental ones. Rooting the haplotype cladogram with a putative primitive haplotype identified Newfoundland and the Queen Charlotte Islands as potential sites of recent refugia. We question whether study of geographic variation in song sparrows leads to insights concerning speciation.
Geographic variation in mitochondrial DNA (mtDNA) restriction sites was studied in the fox sparrow (Passerella iliaca). Seventy-eight haplotypes were found. Haplotypes fall into four phylogeographic groups that correspond to groups defined by plumage characters. The geographic distribution of these four groups does not appear congruent with mtDNA patterns in other vertebrates. Within each group, there is little geographic variation in mtDNA restriction sites, although there is geographic variation in plumage coloration and body size. The evolution of mtDNA diversity in fox sparrows seems best explained by vicariant events rather than isolation by distance. The mtDNA evidence suggests that Passerella megarhyncha and Passerella schistacea, two nonsister taxa that occur in western North America, have independently undergone bottlenecks. Hybridization is limited between all pairs of taxa except P megarhyncha and P. schistacea, where mtDNA evidence suggests a narrow contact zone along the interface of the Great Basin and Sierra Nevada/Cascades. Morphometric characters intergrade over a broader area, suggesting that different processes are responsible for the two gradients. The occurrence of limited backcrossing among taxa suggests that cytoplasmic-nuclear incompatibility is lacking. The number of biological species would range from one to four, depending on the degree of hybridization tolerated. The mtDNA and plumage characters suggest four phylogenetic species: P. iliaca, P. megarhyncha, P. unalaschcensis, and P. schistacea.
AssTnAcr.-We studied restriction site variation in the mitochondrial DNA (mtDNA) of 55 Chipping Sparrows (Spizella passerina) taken from widely dispersed points in their breeding range. A total of 2 1 haplotypes was observed, and on average, individuals differed little in percent haplotype divergence (0.12%). There was no detectable geographic variation in haplotypes, despite the sampling of three named subspecies. Single-generation dispersal distance was estimated from the mtDNA data at 5.4 km. One phylogenetic hypothesis for six species in the genus (excluding Timberline Sparrow [S. taverneri] and Worthen' s Sparrow [S. worthenl]) suggested that Black-chinned Sparrow (S. atroguluris) and Field Sparrow (S. pusilla) were sister taxa, followed in sequence by Chipping, Brewer' s and Clay-colored sparrows (S. pallida), with the American Tree Sparrow (S. arboreu) most distant. Another hypothesis grouped Chipping and Brewer' s sparrows. An important step in the evolutionary process is the origin of geographic patterns of genetic variation. Patterns of genetic variation form the basis for inferences about evolutionary processes that lead to the origin and maintenance of geographic variation and speciation. In the last 20 years, a number of molecular techniques, including protein electrophoresis and restriction site analysis of mitochondrial DNA (mtDNA; Avise et al. 1987), have been used to describe genetic variation within and among avian populations. For north temperate birds, protein electrophoresis revealed few alleles that varied geographically (Barrowclough 1983). From this result, many researchers inferred that avian populations were essentially panmictic, and that gene flow was substantial (Barrowclough 1983, Barrowclough and Johnson 1988). Studies of mtDNA opened a new era because of several advantageous aspects of mtDNA evolution (Moritz et al. 1987). In particular, mtDNA appears to evolve faster than most types of nuclear DNA (including that which encodes allozymes), providing an enhanced probability of detecting geographic variation. Indeed, mtDNA studies reveal an array of population structures (Ball et al.
Quantitative genetic models of phenotypic evolution in small isolated populations are presented, from the initial founding event to continued random genetic drift and natural selection toward a new optimum phenotype. The basic features of complex morphologies included are polygenic inheritance with multiple allelism, pleiotropy, recombination and mutation. Gene flow, inbreeding depression, gene interaction, and genetic homeostasis are also discussed. Simpson's adaptive zones for phenotypes (analogous to Wright's adaptive topography for gene frequencies) are formulated probabilistically for small populations. It is concluded that Mayr's theory of allopatric speciation overemphasized both the genetic cohesion of widespread species and the founder effect on heterozygosity and quantitative genetic variation. However, data on the strength of natural selection and the spontaneous mutability of quantitative characters, in conjunction with the models, provide a feasible microevolutionary mechanism for substantial...
Summary Variation within and between eight subspecies of Canada geese was assessed by restriction fragment analysis of mitochondrial DNA (mtDNA), electrophoresis of proteins encoded by nuclear DNA, and the morphometric analysis of skeletons. Estimates of mtDNA sequence divergence between Canada goose subspecies ranged from 0.04 to 2.54%. Pairwise comparisons of the three data matrices revealed that only mtDNA variation and body size are significantly correlated. Subspecies with northern breeding grounds are small-bodied and display small variations of one mtDNA clone, whereas those breeding further south are largebodied and show small differences in another mtDNA clone. Canada geese exhibit strong geographic differentiation with respect to mtDNA sequence, but weak structuring in protein-encoding nuclear DNA. This finding can be explained by a lower level of gene flow for the mitochondrial genome than for the nuclear genome, which in turn emanates from the maternal inheritance of mtDNA and male-biased dispersal in Canada geese. Despite male-mediated flow of nuclear genes, strong morphometric differentiation persists among Canada geese subspecies.
This study describes the population structure of Norway spruce (Picea abies) as revealed by protein polymorphisms and morphological variation. Electrophoretically detectable genetic variability was examined at 22 protein loci in 70 populations from the natural range of the species in Europe. Like other conifers, Norway spruce exhibits a relatively large amount of genetic variability and little differentiation among populations. Sixteen polymorphic loci (73%) segregate for a total of 51 alleles, and average heterozygosity per population is 0.115. Approximately 5% of the total genetic diversity is explained by differences between populations (GST = 0.052), and Nei's standard genetic distance is less than 0.04 in all cases. We suggest that the population structure largely reflects relatively recent historical events related to the last glaciation and that Norway spruce is still in a process of adaptation and differentiation. There is a clear geographic pattern in the variation of allele frequencies. A major part of the allelefrequency variation can be accounted for by a few synthetic variables (principal components), and 80% of the variation of the first principal component is "explained" by latitude and longitude. The central European populations are consistently depauperate of genetic variability, most likely as an effect of severe restrictions of population size during the last glaciation. The pattern of differentiation at protein loci is very similar to that observed for seven morphological traits examined. This similarity suggests that the same evolutionary forces have acted upon both sets of characters.
Our understanding of the causes of molecular evolution is not as certain as it was a decade ago when Kimura's neutral theory appeared to explain major features of DNA conservation and change. The last ten years have seen the development of empirical approaches and statistical tests for detecting selection in DNA and a proliferation of data that challenge our current understanding of the molecular evolutionary process. We begin this review with a discussion of protein polymorphism and divergence: two major areas of research where the strictly neutral model cannot explain general patterns in the data. We then present a survey of statistical methods for detecting positive selection, which includes tests for balancing selection, for sequence convergence, and for unusually high rates of evolution that cannot be accounted for by neutral models. Finally, we present findings of a number of groups working on within- and between-species variation in Drosophila: These highlight the importance of adaptive evolution, purifying selection, and recombination in understanding levels and patterns of nucleotide variation.
The genetic effects of pleistocene ice ages are approached by deduction from paleoenvironmental information, by induction from the genetic structure of populations and species, and by their combination to infer likely consequences. (1) Recent palaeoclimatic information indicate rapid global reversals and changes in ranges of species which would involve elimination with spreading from the edge. Leading edge colonization during a rapid expansion would be leptokurtic and lead to homozygosity and spatial assortment of genomes. In Europe and North America, ice age contractions were into southern refugia, which would promote genome reorganization. (2) The present day genetic structure of species shows frequent geographic subdivision, with parapatric genomes, hybrid zones and suture zones. A survey of recent DNA phylogeographic information supports and extends earlier work. (3) The grasshopper Chorthippus parallelus is used to illustrate such data and processes. Its range in Europe is divided on DNA sequences into five parapatric races, with southern genomes showing greater haplotype diversity - probably due to southern mountain blocks acting as refugia and northern expansion reducing diversity. (4) Comparison with other recent studies shows a concordance of such phylogeographic data over pleistocene time scales. (5) The role that ice age range changes may have played in changing adaptations is explored, including the limits of range, rapid change in new invasions and refugial differentiation in a variety of organisms. (6) The effects of these events in causing divergence and speciation are explored using Chorthippus as a paradigm. Repeated contraction and expansion would accumulate genome differences and adaptations, protected from mixing by hybrid zones, and such a composite mode of speciation could apply to many organisms.
Expansions of population size leave characteristic signatures in mitochondrial "mismatch distributions." Consequently, these distributions can inform us about the history of changes in population size. Here, I study a simple model of population history that assumes that, t generations before the present, a population grows (or shrinks) suddenly from female size N0 to female size N1. Although this model is simple, it often provides an accurate description of data generated by complex population histories. I develop statistical methods that estimate θ0 = 2uN0, θ1 = 2uN1, and τ = 2ut (where u is the mutation rate), and place a confidence region around these estimates. These estimators are well behaved, and insensitive to simplifying assumptions. Finally, I apply these methods to published mitochondrial data, and infer that a major expansion of the human population occurred during the late Pleistocene.
An optimized reverse transcription (RT)-PCR protocol for the intravitam detection of rabies virus genomic RNA was tested with clinical samples obtained from 28 patients suspected of having rabies, 9 of whom were confirmed to have had rabies by postmortem examination. RT-PCR using saliva combined with an immunofluorescence assay performed with skin biopsy samples allowed detection of rabies in the nine patients.
Variation and change in mitochondrial DNA (mtDNA) is often assumed to conform to a constant mutation rate equilibrium neutral model of molecular evolution. Recent evidence, however, indicates that the assumptions underlying this model are frequently violated. The mitochondria) genome may be subject to the same suite of forces known to be acting in the nuclear genome, including hitchhiking and selection, as well as forces that do not affect nuclear variation. Wherever possible, evolutionary studies involving mtDNA should incorporate statistical tests to investigate the forces shaping sequence variation and evolution.
Comparison of mitochondrial DNA (mtDNA) control-region sequences of 155 dunlins from 15 breeding populations confirmed the existence of five major phylogeographic groups in the circumpolar breeding range of this migratory shorebird species. Time estimates of the origin of groups, based on sequence divergences and a molecular clock for birds, suggest a scenario of repeated fragmentation of populations in isolated tundra refugia during the late Pleistocene. The distribution of about three-quarters of all detected molecular variance between phylogeographic groups attests to the strongly subdivided genetic population structure in dunlins that is being maintained by natal philopatry. Each mtDNA phylogeographic group can be related to a morphometrically defined subspecies, but several other recognized subspecies are not supported by monophyletic mtDNA lineages within their purported ranges. More detailed analysis of several European populations reveals low amounts of gene flow and the partitioning of a substantial fraction of molecular variance between them. This ongoing evolution of population-genetic structuring within the European phylogeographic group most likely started with the last retreat of the ice sheets some 10,000 years ago. Dunlins thus provide one of the clearest examples of the linkage between historical and contemporary components of mtDNA phylogeographic structuring in birds.
A new method for determining nucleotide sequences in DNA is described. It is similar to the "plus and minus" method [Sanger, F. & Coulson, A. R. (1975) J. Mol. Biol. 94, 441-448] but makes use of the 2',3'-dideoxy and arabinonucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase. The technique has been applied to the DNA of bacteriophage varphiX174 and is more rapid and more accurate than either the plus or the minus method.
Restriction endonuclease assay of mitochondria DNA (mtDNA) and standard starch-gel electrophoresis of proteins encoded by nuclear genes have been used to analyze phylogenetic relatedness among a large number of pocket gophers (Geomys pinetis) collected throughout the range of the species. The restriction analysis clearly distinguishes two populations within the species, an eastern and a western form, which differ by at least 3% in mtDNA sequence. Qualitative comparisons of the restriction phenotypes can also be used to identify mtDNA "clones" within each form. The mtDNA clones interconnect in a phylogenetic network which represents an estimate of matriarchal phylogeny for G. pinetis. Although the protein electrophoretic data also differentiate the eastern and western forms, the data are of limited usefulness in establishing relationships among more local subpopulations. The comparison between these two data sets suggests that restriction analysis of mtDNA is probably unequalled by other techniques currently available for determining phylogenetic relationships among conspecific organisms.
The distribution is obtained for the number of segregating sites observed in a sample from a population which is subject to recurring, new, mutations but not subject to recombination. After allowance is made for the different effective population sizes, the results apply approximately to three population models, due to Wright, Burrows and Cockerham, and Moran. Included as extreme special cases are the distributions of the number of segregating sites in the whole population and of the number of heterozygous sites in a diploid individual. Some results of Fisher, Haldane, Kimura, and Ewens concerning the means of the distributions for different models are confirmed, but the variances, and the distributions themselves, are new.
By using the polymerase chain reaction to amplify and sequence 178 bp of a rapidly evolving region of the mtDNA genome (segment I of the control region) from 81 individuals, approximately 11% of the variation present in the lesser snow goose Chen caerulescens caerulescens L. mitochondrial genome was surveyed. The 26 types of mtDNA detected formed two distinct mitochondrial clades that differ by an average of 6.7% and are distributed across the species range. Restriction analysis of amplified fragments was then used to assign the mtDNA of an additional 29 individuals to either of these clades. Within one major clade, sequence among mtDNAs was concordant with geographic location. Within the other major clade the degree of sequence divergence among haplotypes was lower and no consistent geographic structuring was evident. The two major clades presumably result from vicariant separation of lesser snow geese during the Pleistocene.
We consider the distribution of pairwise sequence differences of mitochondrial DNA or of other nonrecombining portions of the genome in a population that has been of constant size and in a population that has been growing in size exponentially for a long time. We show that, in a population of constant size, the sample distribution of pairwise differences will typically deviate substantially from the geometric distribution expected, because the history of coalescent events in a single sample of genes imposes a substantial correlation on pairwise differences. Consequently, a goodness-of-fit test of observed pairwise differences to the geometric distribution, which assumes that each pairwise comparison is independent, is not a valid test of the hypothesis that the genes were sampled from a panmictic population of constant size. In an exponentially growing population in which the product of the current population size and the growth rate is substantially larger than one, our analytical and simulation results show that most coalescent events occur relatively early and in a restricted range of times. Hence, the "gene tree" will be nearly a "star phylogeny" and the distribution of pairwise differences will be nearly a Poisson distribution. In that case, it is possible to estimate r, the population growth rate, if the mutation rate, mu, and current population size, N0, are assumed known. The estimate of r is the solution to ri/mu = ln(N0r) - gamma, where i is the average pairwise difference and gamma approximately 0.577 is Euler's constant.
The proposal that all mitochondrial DNA (mtDNA) types in contemporary humans stem from a common ancestor present in an African
population some 200,000 years ago has attracted much attention. To study this proposal further, two hypervariable segments
of mtDNA were sequenced from 189 people of diverse geographic origin, including 121 native Africans. Geographic specificity
was observed in that identical mtDNA types are shared within but not between populations. A tree relating these mtDNA sequences
to one another and to a chimpanzee sequence has many deep branches leading exclusively to African mtDNAs. An African origin
for human mtDNA is supported by two statistical tests. With the use of the chimpanzee and human sequences to calibrate the
rate of mtDNA evolution, the age of the common human mtDNA ancestor is placed between 166,000 and 249,000 years. These results
thus support and extend the African origin hypothesis of human mtDNA evolution.
Human mitochondrial DNA (mt-DNA) data from 18 populations have been carefully reexamined. A phylogeny of 77 mtDNA types found among the 1389 individuals analyzed for restriction fragment length polymorphisms (RFLPs) was established using the parsimony principle and compared to a UPGMA tree of the 18 populations. Both analyses agreed in separating African samples from the other populations, though the mtDNA type phylogeny suggested close relations between Africans and other continental groups. Conformity of observed mtDNA type frequency distributions with the "infinite allele" model was studied for 31 human populations. Several Oriental and Caucasoid populations were found to be overly homogeneous, generally due to an elevated frequency of one particular type. Contrastingly, all African samples conformed to the neutral model of populations at equilibrium and presented more diversified distributions. This suggested that part of the apparent African divergence was due to heterogeneous evolutionary processes and confirmed that some diversity reducing factors were at work in Caucasoids and Orientals. Several nonexclusive hypotheses accounting for the rejection of the neutrality tests were discussed. Alternative hypotheses concerning modern human emergence were also reviewed in the light of present results.
A recent study of mitochondrial DNA (mtDNA) polymorphism has generated much debate about modern human origins by proposing the existence of an "African Eve" living 200,000 years ago somewhere in Africa. In an attempt to synthesize information concerning human mtDNA genetic polymorphism, all available data on mtDNA RFLP have been gathered. A phylogeny of the mtDNA types found in 10 populations reveals that all types could have issued from a single common ancestral type. The distribution of shared types between continental groups indicates that caucasoid populations could be the closest to an ancestral population from which all other continental groups would have diverged. A partial phylogeny of the types found in five other populations also demonstrates that the myth of an African Eden was based on an incorrect "genealogical tree" of mtDNA types. Two measures of molecular diversity have been computed on all samples on the basis of mtDNA type frequencies, on one hand, and on the basis of the number of polymorphic sites in the samples, on the other. A large discrepancy is found between the two measures except in African populations; this suggests the existence of some differential selective mechanisms. The lapse of time necessary for creating the observed molecular diversity from an ancestral monomorphic population has been calculated and is found generally greater in Oriental and caucasoid populations. Implications concerning human mtDNA evolution are discussed.
The rabies tissue culture infection test (RTCIT) and rapid rabies enzyme immunodiagnosis (RREID) were compared to the fluorescent-antibody test (FAT) with field specimens. At the French National Reference Center for Rabies, 15,248 specimens were analyzed by FAT and RTCIT, and 2,290 of those specimens were also tested by RREID; 818 other specimens were tested by FAT and RREID in 12 laboratories located in Africa, Asia, and Latin America. The sensitivities and specificities of RREID and RTCIT were comparable. This study showed that both tests can be used as backup procedures to confirm FAT. RREID is also strongly recommended for epidemiological studies and for laboratories which are not equipped for performing FAT.
Adult female and juvenile Mexican free-tailed bats (Tadarida brasiliensis mexicana) were collected bimonthly at Lava Cave, New Mexico from May through September. The purpose of this study was to examine the prevalence of active rabies infection as well as to determine individual immune status in these hosts. All bats were bled and examined for rabies antibody (total antibody versus IgM) utilizing a modified serum neutralization test. The brains were removed and examined by the fluorescent rabies antibody (FRA) test. No significant difference was observed in the number of adults with rabies neutralizing antibody (total) over the study period. Significant differences in rabies neutralizing antibody (total) were observed among the juveniles sampled during July and August. The number of adults with IgM specific antibody was low (15 of 750, 2%) and did not fluctuate significantly. However, the number of juveniles with IgM antibody did show increased levels in August and September. The number of adults positive by the FRA was low (4 of 750, less than 1%) and did not appear to fluctuate significantly over the study period. The number of juveniles positive by the FRA was three and one-half times higher than observed for the adults (14 of 600, 2%). These results indicate that the Mexican free-tailed bat appears to be exposed to rabies virus shortly after birth as evident by its immune status. The low prevalence (4 of 750, less than 1%) of active infection as determined by the FRA and mouse inoculation and the high prevalence (514 of 750, 69%) of IgG antibody in the adult females indicate that the Mexican free-tailed bat recovers from rabies virus infection.
The exquisite sensitivity of the polymerase chain reaction means DNA contamination can ruin an entire experiment. Tidiness and adherence to a strict set of protocols can avoid disaster.
Mitochondrial DNAs from 147 people, drawn from five geographic populations have been analysed by restriction mapping. All these mitochondrial DNAs stem from one woman who is postulated to have lived about 200,000 years ago, probably in Africa. All the populations examined except the African population have multiple origins, implying that each area was colonised repeatedly.
A noncoding nuclear DNA marker sequence (Cpn1-1) was used to investigate subdivision in the grasshopper Chorthippus parallelus and deduce postglacial expansion patterns across its species range in Europe. Investigation of the spatial distribution of 71 Cpn1-1 haplotypes and estimation of levels of genetic differentiation (KST values) between populations and geographic regions provided evidence for subdivision of C. parallelus into at least five major geographic regions and indicated that the French form of C. parallelus originated after range expansion from a Balkan refugium. Further evidence for subdivision of C. parallelus between Italy and northern Europe suggests that the Alps may have formed a significant barrier to gene flow in this grasshopper.
We consider the effect on the distribution of pairwise differences between mitochondrial DNA sequences of the incorporation into the underlying population genetics model of two particular effects that seem realistic for human populations. The first is that the population size was roughly constant before growing to its current level. The second is that the population is geographically subdivided rather than panmictic. In each case these features tend to encourage multimodal distributions of pairwise differences, in contrast to existing, unimodal datasets. We argue that population genetics models currently used to analyze such data may thus fail to reflect important features of human mitochondrial DNA evolution. These may include selection on the mitochondrial genome, more realistic mutation mechanisms, or special population or migration dynamics. Particularly in view of the variability inherent in the single available human mitochondrial genealogy, it is argued that until these effects are better understood, inferences from such data should be rather cautious.
Hunting during the last 200 years reduced many populations of mysticete whales to near extinction. To evaluate potential genetic bottlenecks in these exploited populations, we examined mitochondrial DNA control region sequences from 90 individual humpback whales (Megaptera novaeangliae) representing six subpopulations in three ocean basins. Comparisons of relative nucleotide and nucleotype diversity reveal an abundance of genetic variation in all but one of the oceanic subpopulations. Phylogenetic reconstruction of nucleotypes and analysis of maternal gene flow show that current genetic variation is not due to postexploitation migration between oceans but is a relic of past population variability. Calibration of the rate of control region evolution across three families of whales suggests that existing humpback whale lineages are of ancient origin. Preservation of preexploitation variation in humpback whales may be attributed to their long life-span and overlapping generations and to an effective, though perhaps not timely, international prohibition against hunting.
Forty-seven European bat lyssaviruses (EBL) and two African insectivorous bat lyssaviruses (Duvenhage viruses) were selected for a comparison to be made of their evolutionary relationships. Studies were based on direct sequencing of the PCR-amplified products of the 400 nucleotides coding for the amino terminus of the nucleoprotein. Phylogenetic relationships were analysed after bootstrap resampling using the maximum parsimony and the neighbour-joining methods. Analyses of both the nucleotide and amino acid sequences placed these viruses in three separate clusters, namely genotype 4 (Duvenhage), genotype 5 (EBL1) and genotype 6 (EBL2). Evolutionary analysis of the nucleoprotein gene of EBL1 and EBL2 indicated low intrinsic heterogeneity mainly due to synonymous substitutions. In addition, both EBL1 and EBL2 evolved into at least two genetically distinguishable lineages (a and b) following geographical drifting. We can speculate that subsequently the lineages EBL1a and EBL1b were introduced into parts of northern Europe from two different geographical directions; EBL1b was probably introduced most recently and was from North Africa. Eptesicus serotinus appears to be the principal reservoir for EBL1 and Myotis dasycneme and M. daubentonii the reservoirs for EBL2.