Contrasting views over a hybrid complex: Between speciation and evolutionary "dead-end"

The Squalius alburnoides complex, of hybrid origin, comprises diploid, triploid and tetraploid forms and has a widespread distribution in the Iberian waters. The southern populations of this complex, sympatric with S. pyrenaicus, show high genetic variability, diversity of forms and reproductive modes which create pathways that may allow for the establishment of a new species in the future. Here we report a contrasting view over the S. alburnoides complex: in the Mondego River basin (northern Portugal), nuclear "non-hybrid" and tetraploid forms are absent and a clearly impoverished genetic diversity is observed, contributing to a general scarcity of possibilities of generating novel genetic material. Moreover, the bisexual species involved in the maintenance of the complex in this basin (S. carolitertii) exhibits a considerably lower genetic variability, when compared with S. pyrenaicus. The observed differences suggest that, despite being originated by similar hybridization events and maintained by analogous reproductive mechanisms, different populations of the complex were exposed to distinct evolutionary constrains, which in some cases resulted in diversification and speciation while in others led to a compromising situation in terms of evolutionary potential. Additionally, and for the first time all forms were used in the calculation of genetic distances and diversity indices, widening the possibilities of analysis of the complex by allowing the inclusion of a large part of the available data, irrespective of ploidy level.     

Gene expression regulation and lineage evolution: the North and South tale of the hybrid polyploid Squalius alburnoides complex

The evolution of hybrid polyploid vertebrates, their viability and their perpetuation over evolutionary time have always been questions of great interest. However, little is known about the impact of hybridization and polyploidization on the regulatory networks that guarantee the appropriate quantitative and qualitative gene expression programme. The Squalius alburnoides complex of hybrid fish is an attractive system to address these questions, as it includes a wide variety of diploid and polyploid forms, and intricate systems of genetic exchange. Through the study of genome-specific allele expression of seven housekeeping and tissue-specific genes, we found that a gene copy silencing mechanism of dosage compensation exists throughout the distribution range of the complex. Here we show that the allele-specific patterns of silencing vary within the complex, according to the geographical origin and the type of genome involved in the hybridization process. In southern populations, triploids of S. alburnoides show an overall tendency for silencing the allele from the minority genome, while northern population polyploids exhibit preferential biallelic gene expression patterns, irrespective of genomic composition. The present findings further suggest that gene copy silencing and variable expression of specific allele combinations may be important processes in vertebrate polyploid evolution.     

Genetic subdivision, glacial refugia and postglacial recolonization in the golden-striped salamander, Chioglossa lusitanica (Amphibia: urodela)

The golden-striped salamander (Chioglossa lusitanica) is an ecologically specialized species, endemic to north-western Iberia. Patterns of genetic variation were assessed at seven polymorphic enzyme loci and one mitochondrial DNA (mtDNA) marker (cytochrome b) in 17 populations across its range. Estimates of enzyme genetic diversity revealed a high degree of genetic subdivision (FST = 0.68), mainly attributable to the existence of two groups of populations. The groups were located, respectively, north and south of the Mondego River, indicating that this river coincided with a major historical barrier to gene flow. A significant decrease in genetic variability from the Mondego northwards was associated with the Douro and Minho rivers. mtDNA sequence variation revealed a congruent pattern of two haplotype groups (d = 2.2%), with a geographical distribution resembling that of allozymes. The pattern and depth of genetic variation is consistent with the following hypotheses: (i) subdivision of an ancestral range of the species prior to the middle Pleistocene; (ii) secondary contact between populations representing historical refugia; (iii) relatively recent range expansion giving rise to the northern part of the species range; and (iv) loss of genetic variation through founder effects during range expansion across major rivers.     

Genetic variability of the peripheral population of the greater long-tailed hamster <Emphasis Type="Italic">Tscherskia triton</Emphasis> (De Winton 1899) in the northeastern part of the distribution range based on sequencing data of the control region of mitochondrial DNA

The genetic variability of the greater long-tailed hamster Tscherskia triton of the peripheral population of the southern Russian Far East is evaluated compared to the central populations of China based on the nucleotide sequences of the control region of mitochondrial DNA. The high genetic diversity of the population of the southern part of Russian Far East is established, which does not confirm a hypothesis on reduction of the diversity in the peripheral populations. The presence of three phylogroups is discovered: one within Russia (“northern”) and two within China (“central” and “southern”). A deletion, absent in other taxonomically distant groups of the Old and New World and acquired by the greater long-tailed hamster over the course of its evolutionary history, is present in certain populations of this species. A preliminary hypothesis, according to which the contemporary structure of this species is determined not only by topographical and climatic events, but by human activity as well, is formulated.     

Fluctuating asymmetry in populations of British roe deer (Capreolus capreolus) following historical bottlenecks and founder events

The potential impact of population bottlenecks and founder events on genetic diversity and indirect measures of fitness (such as fluctuating asymmetry; FA) has important conservation implications. Here we take advantage of historical events that generated a remnant roe deer (Capreolus capreolus) population in the north of the British Isles that retained diversity, while populations in the south were apparently extirpated during the early mediaeval era. The southern population was later re-established from small founder populations of introduced European roe deer starting in the 19th century. We assess the impact of these events, using the northern remnant population as a reference, based on measures of FA at 16 bilateral cranial traits. Comparing the northern and southern populations we find evidence of differential impact on both the level of FA and the relationship between FA and levels of genetic diversity.     

Genetic Structure and Demographic History Reveal Migration of the Diamondback Moth Plutella xylostella (Lepidoptera: Plutellidae) from the Southern to Northern Regions of China

The diamondback moth Plutella xylostella (Linnaeus) (Lepidoptera: Plutellidae) is one of the most destructive insect pests of cruciferous plants worldwide. Biological, ecological and genetic studies have indicated that this moth is migratory in many regions around the world. Although outbreaks of this pest occur annually in China and cause heavy damage, little is known concerning its migration. To better understand its migration pattern, we investigated the population genetic structure and demographic history of the diamondback moth by analyzing 27 geographical populations across China using four mitochondrial genes and nine microsatellite loci. The results showed that high haplotype diversity and low nucleotide diversity occurred in the diamondback moth populations, a finding that is typical for migratory species. No genetic differentiation among all populations and no correlation between genetic and geographical distance were found. However, pairwise analysis of the mitochondrial genes has indicated that populations from the southern region were more differentiated than those from the northern region. Gene flow analysis revealed that the effective number of migrants per generation into populations of the northern region is very high, whereas that into populations of the southern region is quite low. Neutrality testing, mismatch distribution and Bayesian Skyline Plot analyses based on mitochondrial genes all revealed that deviation from Hardy-Weinberg equilibrium and sudden expansion of the effective population size were present in populations from the northern region but not in those from the southern region. In conclusion, all our analyses strongly demonstrated that the diamondback moth migrates within China from the southern to northern regions with rare effective migration in the reverse direction. Our research provides a successful example of using population genetic approaches to resolve the seasonal migration of insects.     

Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan

Nucleotide sequences of 3' end of the cytochrome b gene, tRNA genes, D-loop control region, and the 5' end of the 12S rRNA of mitochondrial DNA (mtDNA) were used to assess the genetic and phylogeographic structure of Acrossocheilus paradoxus populations, a Cyprinidae fish of Taiwan. A hierarchical examination of populations in 12 major streams from three geographical regions using an analysis of molecular variance (AMOVA) indicates high genetic differentiation both among populations (PhiST = 0.511, P < 0.001) and among regions (PhiCT = 0.368, P < 0.001). Limited migration largely contributed to the genetic differentiation. High nucleotide diversity (1.13%) and haplotype diversity (0.80%) were detected among populations. The degree of genetic differentiation was correlated with geographical distance between populations, a result consistent with the one-dimensional stepping stone models. A neighbour-joining tree recovered by (DAMBE) supports the pattern of isolation by distance and reveals a closer relationship between populations of the central and southern regions. A minimum spanning network based on nucleotide substitutions reflected migration routes from populations of the central region to the northern and southern regions, respectively. Postglacial colonization and expansion can explain the phylogeographical pattern. Single and ancient migration events may have allowed the northern region to attain the monophyly of mtDNA alleles. In contrast, most populations within geographical regions are either paraphyletic or polyphyletic due to the relatively shorter time period for coalescence. Both low haplotype number and genetic variability suggest a bottleneck event in the Chingmei population of northern Taiwan. Based on coalescence theory, the monophyly of the Tungkang population of the southern region may be associated with a founder event.     

Extremely low genetic diversity and extensive genetic admixture at the northern range margins of Bombax ceiba

Understanding the evolutionary processes in species at the margins of their range is of great significance, because marginal populations may harbor local adaptations and will initiate further expansion in response to changes in the environment. Here we examined genetic variation in two nuclear genes and one chloroplast intergenic spacer in 13 northern marginal populations and one geographically central population of Bombax ceiba, a tree distributed mainly in tropical regions. Our results revealed an extremely low level of genetic diversity in each population at the northern margin of its range and strong genetic differentiation between southern China and South Asia. Cultivated and natural populations showed no significant differences in genetic variability. Genetic admixture in a nuclear gene was detected in 10 of the 13 populations at the northern margin of their range. The founder effect, in which a small number of individuals colonize the northern margins of its range, may explain the extremely low genetic diversity. During the establishment of new populations, different source populations may mix and undergo further genetic drift and differentiation. This study indicates that patterns of genetic diversity in tropical species at the margin of their range may also be severely influenced by founder effects.     

Genetic diversity and population divergence in fragmented habitats: Conservation of Idaho ground squirrels

The Idaho ground squirrel, which consists of a northern (Spermophilus brunneus brunneus) and a southern subspecies (S. b. endemicus), has suffered from habitat loss and fragmentation, resulting in a reduction in both numbers and geographic range of the species. The northern Idaho ground squirrel (NIDGS) is listed as a threatened subspecies under the Endangered Species Act, and the southern Idaho ground squirrel (SIDGS) is a candidate. Because Idaho ground squirrel populations are small and often isolated, they are susceptible to inbreeding and loss of genetic diversity through drift. This research evaluates levels of genetic diversity and patterns of population divergence in both subspecies of Idaho ground squirrels. We hypothesized that NIDGS would exhibit lower genetic diversity and greater population divergence due to a longer period of population isolation relative to most SIDGS populations. Genetic diversity and divergence were quantified using 8 microsatellite loci. Contrary to expectations, SIDGS populations exhibited consistently lower levels of microsatellite diversity. Additionally, NIDGS exhibited only modest divergence among populations, while divergence levels among SIDGS populations were highly varied. Preliminary evaluations of mitochondrial DNA diversity and structure revealed lower diversity in NIDGS and some differences in gene flow that warrant further study. Based on our results, we suggest different management strategies for the two subspecies. Habitat restoration appears to be the most desirable conservation strategy for NIDGS populations. In contrast, low genetic diversity observed in SIDGS may warrant supplementation of isolated populations through translocations or captive breeding to mitigate further loss of genetic variability.     

Strong intraspecific variation in genetic diversity and genetic differentiation in Daphnia magna: the effects of population turnover and population size

Theory predicts that genetic diversity and genetic differentiation may strongly vary among populations of the same species depending on population turnover and local population sizes. Yet, despite the importance of these predictions for evolutionary and conservation issues, empirical studies comparing high‐turnover and low‐turnover populations of the same species are scarce. In this study, we used Daphnia magna, a freshwater crustacean, as a model organism for such a comparison. In the southern/central part of its range, D. magna inhabits medium‐sized, stable ponds, whereas in the north, it occurs in small rock pools with strong population turnover. We found that these northern populations have a significantly lower genetic diversity and higher genetic differentiation compared to the southern/central populations. Total genetic diversity across populations was only about half and average within‐population diversity only about a third of that in southern/central populations. Moreover, an average southern population contains more genetic diversity than the whole metapopulation system in the north. We based our analyses both on silent sites and microsatellites. The similarity of our results despite the contrasting mutation rates of these markers suggests that the differences are caused by contemporary rather than by historical processes. Our findings show that variation in population turnover and population size may have a major impact on the genetic diversity and differentiation of populations, and hence may lead to differences in evolutionary processes like local adaptation, hybrid vigour and breeding system evolution in different parts of a species range.     

Differential levels of genetic diversity and divergence among populations of an ancient Australian rainforest conifer, Araucaria cunninghamii

Historical fragmentation and subsequent isolation has affected the levels of genetic diversity in many lineages of ancient plant taxa. This study investigated the effects of historical processes on Araucaria cunninghamii (Hoop Pine), Araucariaceae, using both RAPD and ISSR markers. While most populations maintain moderate levels of diversity, there is some evidence for reduced genetic variation. Most sampled populations are significantly differentiated from each other, thereby emphasizing the high degree of population structuring in A. cunninghamii. Increased divergence among the northern Queensland populations relative to southern Queensland populations suggests historical pressures have impacted differently on extant population distribution. More research is specifically required into the biology and population demographics of Australian Araucariaceae.     

POPULATION STRUCTURE OF DIPODOMYS INGENS (HETEROMYIDAE): THE ROLE OF SPATIAL HETEROGENEITY IN MAINTAINING GENETIC DIVERSITY

The giant kangaroo rat, Dipodomys ingens (Heteromyidae), is an endangered rodent that inhabits approximately 3% of its estimated historic range. Its current distribution is centered in two geographic areas, situated about 150 km apart, in south-central California. We sequenced a 293 base-pair fragment at the 5' end of the control region in 95 giant kangaroo rats from nine localities to examine the genetic structure of extant populations. We determine that mutations in this section of the control region follow a negative binominal distribution, rather than a Poisson. However, the distance between haplotypes is small enough that the difference between a tree that corrects for the non-Poisson distribution of mutations and one that does not, is minimal. This implies that the use of methods that assume a Poisson distribution of mutations, such as those based on coalescent theory, are justified. We find that the correlation between levels of genetic diversity and estimated census size is poor. This suggests that population sizes have fluctuated over time or that populations have not been isolated from one another, or both. We also examine the hierarchical structure of populations and find that the southern populations are not genetically subdivided but that there is significant subdivision between northern and southern populations and between some northern subpopulations. The phylogeographic relationship between northern and southern populations can primarily be attributed to isolation by distance, although the time since divergence between them appears to be less than the age of either. To examine the phylogeographic relationships in more detail we construct a minimum spanning tree based on Tamura-Nei gamma-corrected distances and superimpose on it the geographic position of haplotypes. This reveals that there is more genetic distance between some northern haplotypes than between any northern and southern haplotypes, despite the geographic distance separating north from south and the larger size of the southern population. It also reveals that one northern population, in the Panoche Valley, contains old allelic lineages and shares ancestral polymorphism with several other populations. It also shows that two, small, geographically remote populations contain a surprising amount of genetic diversity, but that different population/geographic processes have affected the structure of that diversity. We estimate the average migration rate among all populations to be 7.5 per generation, and conclude that a disproportionate number of migration events involve gene flow with one northern population, the Panoche Valley. We find evidence for the hypothesis that there has been an increase in population size in the remaining populations in the north and suggest that the Panoche Valley could play a role in these expansions. Finally we discuss the probabilitiy that the genetic structure of the southern populations has been affected by fluctuations in size. These results are briefly compared to other studies on the genetic structure of rodent populations.     

MATERNAL ANCESTRY OF THE RUTILUS ALBURNOIDES COMPLEX (TELEOSTEI,CYPRINIDAE) AS DETERMINED BY ANALYSIS OF CYTOCHROME b SEQUENCES

Cytochrome b (cyt b) sequences from specimens of the Rutilus alburnoides unisexual complex and five bisexual species were compared to examine hypotheses regarding the origin and maternal ancestry of this complex. Phylogenetic analysis revealed a monophyletic relationship among unisexuals and Leuciscus pyrenaicus, clearly identifying this species as the maternal ancestor. Considerable mtDNA diversity exists among R. alburnoides populations, with many localities exhibiting unique haplotypes. The topology recovered from analysis of cyt b variation among populations suggested that R. alburnoides is polyphyletically derived from their sympatric L. pyrenaicus populations, indicating that unisexual lineages have been generated through multiple hybridization events. Although much less abundant, R. alburnoides is present outside the range of L. pyrenaicus, suggesting that it may have dispersed from the Tejo drainage into the northern basins. In this region, Leuciscus carolitertii is most likely the sexual host for the unisexual complex.     

Diversity of Arabidobsis thaliana (L.) Heynh. natural populations at the northern limits of the species range: RAPD analysis

In natural populations of Arabidobsis thaliana (L.) Heynh., occupying northern limits of the species range (Karelia), the level of genetic diversity was evaluated. In two insular and one mainland population variability at 82 RAPD loci was tested. Considerable genetic diversity revealed (P = 4.5%; H _exp = 0.177) was not typical of self-pollinating plant species. It was demonstrated that genetic differentiation among the populations (G _ST = 0.680) was rather high, pointing to the low level of gene flow in the isolated insular populations. It was suggested that the high level of Arabidopsis population polymorphism in Karelia could be associated with extreme growing conditions at the northern limits of the species range.     

Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus)

Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super‐volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co‐distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target‐capture data (~950 loci and ~440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction‐site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full‐likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (~80 kya). However, we infer a stronger signal of expansion in southern populations around ~400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid‐Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.     

Genetic diversity and structure of natural fragmented Chamaecyparis obtusa populations as revealed by microsatellite markers

The genetic diversity and population structure of hinoki (Chamaecyparis obtusa) in Japan were investigated by examining the distribution of alleles at 13 microsatellite loci in 25 natural populations from Iwaki in northern Japan to Yakushima Island in southern Japan. On average, 26.9 alleles per locus were identified across all populations and 4.0% of the genetic variation was retained among populations (G _ST = 0.040). According to linkage disequilibrium analysis, estimates of effective population size and detected evidence of bottleneck events, the genetic diversity of some populations may have declined as a result of fragmentation and/or over-exploitation. The central populations located in the Chubu district appear to have relatively large effective population sizes, while marginal populations, such as the Yakushima, Kobayashi and Iwaki populations, have smaller effective population sizes and are isolated from the other populations. Microsatellite analysis revealed the genetic uniqueness of the Yakushima population. Although genetic differentiation between populations was low, we detected a gradual cline in the genetic structure and found that locus Cos2619 may be non-neutral with respect to natural selection.     

Is the genetic diversity of small scattered forest tree populations at the southern limits of their range more prone to stochastic events? A wild cherry case study by microsatellite-based markers

Wild cherry (Prunus avium L.) is a widespread, partially asexual, noble hardwood European species characterized by a scattered distribution, small population sizes, and human exploitation for its valuable wood. These characteristics, especially at the southern limits of the species natural distribution where additional varying stresses may occur, render P. avium populations prone to potential stochastic, genetic, and demographic events. In this study, we used dominant inter simple sequence repeat (ISSR) and codominant simple sequence repeat (SSR) markers to infer the genetic structure of P. avium. Five populations from northern Greece were evaluated based on 46 ISSR and 11 SSR loci. Populations presented a relatively high level of genetic variation, with a mean genetic diversity of H _e?=?0.166 and H _e?=?0.740 regarding ISSR and SSR analysis, respectively. We observed moderate population differentiation for ISSR (G _ST?=?0.113) and SSR (F _ST?=?0.097) markers. AMOVA also detected significant differentiation among populations for ISSRs (?? _ST?=?0.338) and SRRs (?? _ST?=?0.162). According to linkage disequilibrium analysis, estimates of effective population size were generally sufficient for maintaining extant genetic variability and evolutionary potential. A possible bottleneck was detected for only one population. In general, it appears that despite the particular characteristics of the P. avium populations studied, genetic stochasticity events were not apparent. The studied populations, located at the rear edge of the species European distribution, reveal a wealth of genetic variation that is very valuable for the genetic conservation of local adaptive gene complexes, especially under contemporary climatic change scenarios.     

Allozyme diversity and history of distribution expansion in the maritime perennial plant Hedyotis strigulosa (Rubiaceae), distributed over the wide latitudes in the Japanese Archipelago

Allozyme diversity was examined in 30 populations of the maritime perennial plant Hedyotis strigulosa var. parviflora , which is distributed from subtropical islands to the central mainland of Japan. Genetic diversity within populations tended to be larger in southern island populations than in northern mainland populations. In the southern part of the distribution, the population size is generally large and populations are distributed more continuously than in the northern area, resulting in the larger effective size of southern populations as a whole. These factors play a major role in maintaining greater genetic diversity in the southern populations. By contrast, genetic diversity in the northern populations is very low, probably resulting from bottlenecks of population establishments during recolonization from refugial area to the northern areas. Geographically close populations were located near each other in the multidimensional scaling and the phenogram based on genetic distances, suggesting that gene flow among remote populations is rather limited. The pattern of genetic diversity in H. strigulosa var. parviflora is likely caused by the distribution expansion of the species; in the last glacier era, the species was restricted to the southern area; its advance to the northern area is relatively recent. Another variety endemic only to the Daito Islands, H. strigulos a var. luxurians , has lower genetic diversity than H. strigulosa var. parviflora and has genetically diverged from H. strigulosa var. parviflor a.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 679–688.     

Genetic and morphological differentiation in the clam Coelomactra antiquata (Bivalvia: Veneroida) along the coast of China

Coelomactra antiquata is a commercially exploited bivalve, and its populations have been severely declining in the coast of China during the last two decades. In order to provide guidelines for conservation strategies and management programs, four populations of C. antiquata, representing the most important populations in China, were analysed morphologically and genetically to reveal the genetic structure by using 7 polymorphic allozyme loci and 12 morphological variables. The mean allele richness ranged from 2.79 to 3.53, while the mean heterozygosity ranged from 0.326 to 0.519. All genetic distance metrics revealed high level of genetic differentiation between the three northern populations and one southern population. The marked genetic differentiation can be explained by the freshwater outflow of Yangtze River and upwelling of Zhejiang province. The morphological analyses were in accordance with the allozyme data, which also disclosed a high degree of differentiation between the northern and southern populations. The results obtained in this study indicate that the northern and southern populations in C. antiquata should be treated as separate units for conservation management.     

Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia

Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher‐altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.