Evolution of bird song affects signal efficacy: an experimental test using historical and current signals

Mating signals act as behavioral barriers to gene flow in many animal taxa, yet little is known about how signal evolution within populations contributes to the formation of these barriers. Although variation in mating signals among populations is known to affect mating behavior, there is no direct evidence that the evolution of mating signals changes signal effectiveness within a natural population. Making use of historical recordings of bird song, I found that both male and female white-crowned sparrows (Zonotrichia leucophrys) respond more strongly to current than to historical songs, indicating that historical songs are less effective as signals in the current contexts of both mate choice and male-male competition. Finding that historical signals are less effective suggests that signal evolution within populations may ultimately contribute to the formation of behavioral barriers to gene flow between populations.     

Dispersal Pathways and Genetic Differentiation among Worldwide Populations of the Invasive Weed Centaurea solstitialis L. (Asteraceae)

The natural history of introduced species is often unclear due to a lack of historical records. Even when historical information is readily available, important factors of the invasions such as genetic bottlenecks, hybridization, historical relationships among populations and adaptive changes are left unknown. In this study, we developed a set of nuclear, simple sequence repeat markers and used these to characterize the genetic diversity and population structure among native (Eurasian) and non-native (North and South American) populations of Centaurea solstitialis L., (yellow starthistle). We used these data to test hypotheses about the invasion pathways of the species that were based on historical and geographical records, and we make inferences about historical relationships among populations and demographic processes following invasion. We confirm that the center of diversity and the native range of the species is likely the eastern Mediterranean region in the vicinity of Turkey. From this region, the species likely proceeded to colonize other parts of Europe and Asia via a slow, stepwise range expansion. Spanish populations were the primary source of seed to invade South America via human-mediated events, as was evident from historical records, but populations from the eastern Mediterranean region were also important. North American populations were largely derived from South America, but had secondary contributors. We suggest that the introduction history of non-native populations from disparate parts of the native range have allowed not just one, but multiple opportunities first in South America then again in North America for the creation of novel genotypes via intraspecific hybridization. We propose that multiple intraspecific hybridization events may have created especially potent conditions for the selection of a noxious invader, and may explain differences in genetic patterns among North and South America populations, inferred differences in demographic processes, as well as morphological differences previously reported from common garden experiments.     

Low worldwide genetic diversity in the killer whale (Orcinus orca): implications for demographic history

A low level of genetic variation in mammalian populations where the census population size is relatively large has been attributed to various factors, such as a naturally small effective population size, historical bottlenecks and social behaviour. The killer whale (Orcinus orca) is an abundant, highly social species with reduced genetic variation. We find no consistent geographical pattern of global diversity and no mtDNA variation within some regional populations. The regional lack of variation is likely to be due to the strict matrilineal expansion of local populations. The worldwide pattern and paucity of diversity may indicate a historical bottleneck as an additional factor.     

Multiple introductions,admixture and bridgehead invasion characterize the introduction history of Ambrosia artemisiifolia in Europe and Australia

Admixture between differentiated populations is considered to be a powerful mechanism stimulating the invasive success of some introduced species. It is generally facilitated through multiple introductions; however, the importance of admixture prior to introduction has rarely been considered. We assess the likelihood that the invasive Ambrosia artemisiifolia populations of Europe and Australia developed through multiple introductions or were sourced from a historical admixture zone within native North America. To do this, we combine large genomic and sampling data sets analysed with approximate Bayesian computation and random forest scenario evaluation to compare single and multiple invasion scenarios with pre‐ and postintroduction admixture simultaneously. We show the historical admixture zone within native North America originated before global invasion of this weed and could act as a potential source of introduced populations. We provide evidence supporting the hypothesis that the invasive populations established through multiple introductions from the native range into Europe and subsequent bridgehead invasion into Australia. We discuss the evolutionary mechanisms that could promote invasiveness and evolutionary potential of alien species from bridgehead invasions and admixed source populations.     

Genetic variation over space and time: analyses of extinct and remnant lake trout populations in the Upper Great Lakes

Lake trout (Salvelinus namaycush) in the upper Laurentian Great Lakes of North America experienced striking reductions in abundance and distribution during the mid-twentieth century. Complete collapse of populations was documented for Lake Michigan, and a few remnant populations remained only in lakes Huron and Superior. Using DNA obtained from historical scale collections, we analysed patterns of genetic diversity at five microsatellite loci from archived historical samples representing 15 populations (range 1940-1959) and from three contemporary remnant populations across lakes Huron and Superior (total n = 893). Demographic declines in abundance and the extirpation of native lake trout populations during the past 40 years have resulted in the loss of genetic diversity between lakes owing to extirpation of Lake Michigan populations and a temporal trend for reduction in allelic richness in the populations of lakes Superior and Huron. Naturally reproducing populations in Lake Superior, which had been considered to be remnants of historical populations, and which were believed to be responsible for the resurgence of lake trout numbers and distribution, have probably been affected by hatchery supplementation.     

Comparative Population Genomics of African Montane Forest Mammals Support Population Persistence across a Climatic Gradient and Quaternary Climatic Cycles

The Eastern Afromontane biodiversity hotspot (EABH) has the highest concentration of biodiversity in tropical Africa, yet few studies have investigated recent historical diversification processes in EABH lineages. Herein, we analyze restriction-site associated DNA-sequences (RAD-Seq) to study recent historical processes in co-distributed mouse (Hylomyscus) and shrew (Sylvisorex) species complexes, with an aim to better determine how historical paleoenvironmental processes might have contributed to the EABH’s high diversity. We analyzed complete SNP matrices of > 50,000 RAD loci to delineate populations, reconstruct the history of isolation and admixture, and discover geographic patterns of genetic partitioning. These analyses demonstrate that persistently unsuitable habitat may have isolated multiple populations distributed across montane habitat islands in the Itombwe Massif and Albertine Rift to the west as well as Mt Elgon and Kenyan Highlands to the east. We detected low genetic diversity in Kenyan Highland populations of both genera, consistent with smaller historical population sizes in this region. We additionally tested predictions that Albertine Rift populations are older and more persistently isolated compared to the Kenyan Highlands. Phylogenetic analyses support greater historical isolation among Albertine Rift populations of both shrews and mice compared to the Kenyan Highlands and suggest that there are genetically isolated populations from both focal genera in the Itombwe Massif, Democratic Republic of Congo. The Albertine Rift ecoregion has the highest mammalian tropical forest species richness per unit area on earth. Our results clearly support accelerating efforts to conserve this diversity.     

Gene flow, historical population dynamics and genetic diversity within French Guianan populations of a rainforest tree species, Vouacapoua americana

Both gene flow and historical events influence the genetic diversity of natural populations. One way to understand their respective impact is to analyze population genetic structure at large spatial scales. We studied the distribution of genetic diversity of 17 populations of Vouacapoua americana (Caesalpiniaceae) in French Guiana, using nine microsatellite loci. Low genetic diversity was observed within populations, with a mean allelic richness and gene diversity of 4.1 and 0.506, respectively, which could be due to low effective population size and/or past bottlenecks. Using the regression between Fst/(1-Fst), estimated between pairs of populations, and the logarithm of the geographical distance, the spatial genetic structure can partly be explained by isolation-by-distance and limited gene flow among populations. This result is in agreement with the species' biology, including seed and pollen dispersal by rodents and insects, respectively. In contrast, no clear genetic signal of historical events was found when examining genetic differentiation among populations in relation to biogeographical hypotheses or by testing for bottlenecks within populations. Our conclusion is that nuclear spatial genetic structure of V. americana, at the geographic scale of French Guiana, is better explained by gene flow rather than by historical events.     

Mitochondrial DNA and allozymes reveal high dispersal abilities and historical movement across drainage boundaries in two species of freshwater fishes from inland rivers in Queensland, Australia

This study used allozymes and mtDNA variation to test that: 1) populations of two fish species, Nematolosa erebi and Retropinna semoni , in lowland rivers in central Australia were highly connected within drainages, 2) populations in different drainages were highly differentiated and 3) there was evidence of historical connections between two major lowland drainages in inland Australia. Levels of genetic differentiation among populations within drainages were low, but still statistically significant, indicating that populations were not as highly connected as had been predicted. Populations from the Murray–Darling and the Lake Eyre drainages were highly differentiated, indicating no contemporary dispersal across drainage boundaries. Both species showed evidence of historical connections between the two drainage basins, although estimates of the time that these last occurred differed between the two species. Nematolosa erebi populations from the two drainages were estimated to have been separated c . 150 000 years ago, whereas populations of R. semoni , were estimated to have been separated c . 1.5 million years ago.     

Brown trout population structure highly affected by multiple stocking and river diversion in a high mountain national park

Stocking is a widely applied practice for enhancement of fish populations exploited for recreational and commercial uses. In the present study, we investigate the genetic consequences of stocking and river diversion by analyzing 18 microsatellites in 440 brown trout (Salmo trutta L.) from three historical and ten contemporary populations from two river systems in a national park in Norway. Eight sources have been recorded for stocking in this area, but not concurrently. These stocking events took place after historical sampling and river diversion by construction of a barrier and a channel. A complete shift in the genetic structure between historical and contemporary populations was revealed. The genetic differentiation can be explained by stocking with just four non-native sources. The constructed barrier has helped to maintain a fraction of the historical genetic profile. Stocking success is discussed in relation to population exploitation, variation in natural recruitment, and reduced discharge due to river diversion. Our study demonstrates a high vulnerability of natural populations to stocking with non-native fish, of particular importance for fishery management and preservation of native fish.     

Climate change disrupts local adaptation and favours upslope migration

Contemporary climate change is proceeding at an unprecedented rate. The question remains whether populations adapted to historical conditions can persist under rapid environmental change. We tested whether climate change will disrupt local adaptation and reduce population growth rates using the perennial plant Boechera stricta (Brassicaceae). In a large‐scale field experiment conducted over five years, we exposed > 106 000 transplants to historical, current, or future climates and quantified fitness components. Low‐elevation populations outperformed local populations under simulated climate change (snow removal) across all five experimental gardens. Local maladaptation also emerged in control treatments, but it was less pronounced than under snow removal. We recovered local adaptation under snow addition treatments, which reflect historical conditions. Our results revealed that low elevation populations risk rapid decline, whereas upslope migration could enable population persistence and expansion at higher elevation locales. Local adaptation to historical conditions could increase vulnerability to climate change, even for geographically widespread species.     

Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

Invasive plants provide ample opportunity to study evolutionary shifts that occur after introduction to novel environments. However, although genetic characters pre‐dating introduction can be important determinants of later success, large‐scale investigations of historical genetic structure have not been feasible. Common ragweed (Ambrosia artemisiifolia L.) is an invasive weed native to North America that is known for its allergenic pollen. Palynological records from sediment cores indicate that this species was uncommon before European colonization of North America, and ragweed populations expanded rapidly as settlers deforested the landscape on a massive scale, later becoming an aggressive invasive with populations established globally. Towards a direct comparison of genetic structure now and during intense anthropogenic disturbance of the late 19th century, we sampled 45 natural populations of common ragweed across its native range as well as historical herbarium specimens collected up to 140 years ago. Bayesian clustering analyses of 453 modern and 473 historical samples genotyped at three chloroplast spacer regions and six nuclear microsatellite loci reveal that historical ragweed's spatial genetic structure mirrors both the palaeo‐record of Ambrosia pollen deposition and the historical pattern of agricultural density across the landscape. Furthermore, for unknown reasons, this spatial genetic pattern has changed substantially in the intervening years. Following on previous work relating morphology and genetic expression between plants collected from eastern North America and Western Europe, we speculate that the cluster associated with humans’ rapid transformation of the landscape is a likely source of these aggressive invasive populations.     

Population genetics and the evolution of geographic range limits in an annual plant

Abstract Theoretical models of species' geographic range limits have identified both demographic and evolutionary mechanisms that prevent range expansion. Stable range limits have been paradoxical for evolutionary biologists because they represent locations where populations chronically fail to respond to selection. Distinguishing among the proposed causes of species' range limits requires insight into both current and historical population dynamics. The tools of molecular population genetics provide a window into the stability of range limits, historical demography, and rates of gene flow. Here we evaluate alternative range limit models using a multilocus data set based on DNA sequences and microsatellites along with field demographic data from the annual plant Clarkia xantiana ssp. xantiana. Our data suggest that central and peripheral populations have very large historical and current effective population sizes and that there is little evidence for population size changes or bottlenecks associated with colonization in peripheral populations. Whereas range limit populations appear to have been stable, central populations exhibit a signature of population expansion and have contributed asymmetrically to the genetic diversity of peripheral populations via migration. Overall, our results discount strictly demographic models of range limits and more strongly support evolutionary genetic models of range limits, where adaptation is prevented by a lack of genetic variation or maladaptive gene flow.     

Multiple Mantel tests and isolation-by-distance, taking into account long-term historical divergence

Mantel tests of matrix correspondence have been widely used in population genetics to examine microevolutionary processes, such as isolation-by-distance (IBD). We used partial and multiple Mantel tests to simultaneously test long-term historical effects and current divergence and equilibrium processes, such as IBD. We used these procedures to calculate genetic divergence among Eugenia dysenterica (Myrtaceae) populations in Central Brazil. The Nei's genetic distances between pairs of local populations were strongly correlated with geographic distances, suggesting an IBD process, but field observations and the geographic distribution of the samples suggest that populations may have been subjected to more complex evolutionary processes of genetic divergence. Partial Mantel regression was used to partition the effects of geographic structure and long-term divergence associated with a possible historical barrier. The R(2) of the model with both effects was 73.3%, and after the partition 21.9% of the variation in the genetic distances could be attributed to long-term historical divergence alone, whereas only 1.5% of the variation in genetic distances could be attributed to IBD. As expected, there was a large overlap between these processes when explaining genetic divergence, so it was not possible to entirely partition divergence between historical and contemporary processes.     

Looking back to go forward: genetics informs future management of captive and reintroduced populations of the black-footed rock-wallaby <Emphasis Type="Italic">Petrogale lateralis</Emphasis>

Active management is essential to the survival of many threatened species globally. Captive breeding programmes can play an important role in facilitating the supplementation, translocation and reintroduction of wild populations. However, understanding the genetic dynamics within and among wild and captive populations is crucial to the planning and implementation of ex situ management, as adaptive potential is, in part, driven by genetic diversity. Here, we use 14 microsatellite loci and mitochondrial Control Region sequence to examine the population genetics of both wild populations and captive colonies of the endangered warru (the MacDonnell Ranges race of the black-footed rock-wallaby Petrogale lateralis) in central Australia, to understand how historical evolutionary processes have shaped current diversity and ensure effective ex situ management. Whilst microsatellite data reveal significant contemporary differentiation amongst remnant warru populations, evidence of contemporary dispersal and relatively weak isolation by distance, as well as a lack of phylogeographic structure suggests historical connectivity. Genetic diversity within current captive populations is lower than in the wild source populations. Based on our genetic data and ecological observations, we predict outbreeding depression is unlikely and hence make the recommendation that captive populations be managed as one genetic group. This will increase genetic diversity within the captive population and as a result increase the adaptive potential of reintroduced populations. We also identify a new site in the Musgrave Ranges which contains unique alleles but also connectivity with a population 6 km away. This novel genetic diversity could be used as a future source for supplementation.     

Heterozygosity–fitness correlations and their relevance to studies on inbreeding depression in threatened species

The majority of reported multilocus heterozygosity–fitness correlations (HFCs) are from large, outbred populations, and their relevance to studies on inbreeding depression in threatened populations is often stressed. The results of such HFC studies conducted on outbred populations may be of limited application to threatened population management, however, as bottlenecked populations exhibit increased incidence of inbreeding, increased linkage disequilibrium, reduced genetic diversity and possible effects of historical inbreeding such as purging. These differences may affect both our ability to detect inbreeding depression in threatened species, and our interpretation of the underlying mechanisms for observed heterozygosity–fitness relationships. The study of HFCs in outbred populations is of interest in itself, but the results may not translate directly to threatened populations that have undergone severe bottlenecks.     

Spatial and temporal determinants of genetic structure in Gentianella bohemica

The biennial plant Gentianella bohemica is a subendemic of the Bohemian Massif, where it occurs in seminatural grasslands. It has become rare in recent decades as a result of profound changes in land use. Using amplified fragment length polymorphisms (AFLP) fingerprint data, we investigated the genetic structure within and among populations of G. bohemica in Bavaria, the Czech Republic, and the Austrian border region. The aim of our study was (1) to analyze the genetic structure among populations and to discuss these findings in the context of present and historical patterns of connectivity and isolation of populations, (2) to analyze genetic structure among consecutive generations (cohorts of two consecutive years), and (3) to investigate relationships between intrapopulational diversity and effective population size (N(e)) as well as plant traits. (1) The German populations were strongly isolated from each other (pairwise F(ST)= 0.29-0.60) and from all other populations (F(ST)= 0.24-0.49). We found a pattern of near panmixis among the latter (F(ST)= 0.15-0.35) with geographical distance explaining only 8% of the genetic variance. These results were congruent with a principal coordinate analysis (PCoA) and analysis using STRUCTURE to identify genetically coherent groups. These findings are in line with the strong physical barrier and historical constraints, resulting in separation of the German populations from the others. (2) We found pronounced genetic differences between consecutive cohorts of the German populations (pairwise F(ST)= 0.23 and 0.31), which can be explained by local population history (land use, disturbance). (3) Genetic diversity within populations (Shannon index, H(Sh)) was significantly correlated with N(e) (R(S)= 0.733) and reflected a loss of diversity due to several demographic bottlenecks. Overall, we found that the genetic structure in G. bohemica is strongly influenced by historical periods of high connectivity and isolation as well as by marked demographic fluctuations in declining populations.     

Similarity of contemporary and historical gene flow among highly fragmented populations of an endangered rattlesnake

Populations of endangered taxa in recently fragmented habitats often show high levels of genetic structure, but the role that contemporary versus historical processes play in generating this pattern is unclear. The eastern massasauga rattlesnake (Sistrurus c. catenatus) is an endangered snake that presently occurs throughout central and eastern North America in a series of populations that are isolated because of habitat fragmentation and destruction. Here, we use data from 19 species-specific microsatellite DNA loci to assess the levels of genetic differentiation, genetic effective population size, and contemporary and historical levels of gene flow for 19 populations sampled across the range of this snake. Eastern massasaugas display high levels of genetic differentiation (overall θ(Fst) = 0.21) and a Bayesian clustering method indicates that each population represents a unique genetic cluster even at regional spatial scales. There is a twofold variation in genetically effective population sizes but little genetic evidence that populations have undergone recent or historical declines in size. Finally, both contemporary and historical migration rates among populations were low and similar in magnitude even for populations located <7 km apart. A test of alternate models of population history strongly favours a model of long-term drift-migration equilibrium over a recent isolation drift-only model. These results suggest that recent habitat fragmentation has had little effect on the genetic characteristics of these snakes, but rather that this species has historically existed in small isolated populations that may be resistant to the long-term negative effects of inbreeding.     

Microbes, warfare, religion, and human institutions

A significant number of practicing microbiologists are not aware of the historical impact of infectious agents on the development of human institutions. Microbes have played a profound role in warfare, religion, migration of populations, art, and in diplomacy. Boundaries of nations have changed as a result of microbial diseases. Infectious agents have terminated some kingdoms and elevated others. There is a need for microbiologists to have a historical perspective of some of the major ways in which a pathogen may influence civilized populations. Conditions may exist in contemporary society for a repeat of some of the kinds of plagues suffered by previous societies. The purpose of this paper is to review examples of situations where pathogenic microbes have forced societal modifications on centers of human population.     

Contemporary and historic factors influence differently genetic differentiation and diversity in a tropical palm

Population genetics theory predicts loss in genetic variability because of drift and inbreeding in isolated plant populations; however, it has been argued that long-distance pollination and seed dispersal may be able to maintain gene flow, even in highly fragmented landscapes. We tested how historical effective population size, historical migration and contemporary landscape structure, such as forest cover, patch isolation and matrix resistance, affect genetic variability and differentiation of seedlings in a tropical palm (Euterpe edulis) in a human-modified rainforest. We sampled 16 sites within five landscapes in the Brazilian Atlantic forest and assessed genetic variability and differentiation using eight microsatellite loci. Using a model selection approach, none of the covariates explained the variation observed in inbreeding coefficients among populations. The variation in genetic diversity among sites was best explained by historical effective population size. Allelic richness was best explained by historical effective population size and matrix resistance, whereas genetic differentiation was explained by matrix resistance. Coalescence analysis revealed high historical migration between sites within landscapes and constant historical population sizes, showing that the genetic differentiation is most likely due to recent changes caused by habitat loss and fragmentation. Overall, recent landscape changes have a greater influence on among-population genetic variation than historical gene flow process. As immediate restoration actions in landscapes with low forest amount, the development of more permeable matrices to allow the movement of pollinators and seed dispersers may be an effective strategy to maintain microevolutionary processes.     

Substantial genetic structure among stocked and native populations of the European grayling (<Emphasis Type="Italic">Thymallus thymallus</Emphasis>, Salmonidae) in the United Kingdom

While currently in a state of recovery in the United Kingdom (UK), the grayling (Thymallus thymallus) remains of conservation interest due to its historical decline, socio-economic value and the potential impact of hatchery-reared stock fish on the genetic structure and diversity of wild populations. However, little is known about the levels and distribution of genetic diversity among UK grayling populations. To this end, 27 UK populations of grayling were genotyped across 10 microsatellite loci and sequenced at the mtDNA D-Loop. All populations clustered into four higher-level groups: Northern England, Southern England, Wales, and group consisting of a mixture of native and introduced populations. Ten populations showed evidence of bottleneck or founder effects, and the effective population size (Ne) was low in all populations. In most cases, historical stocking records agreed with the genetic relationships revealed in the study. A D-Loop haplotype network supported the groupings observed in the nuclear data, while phylogenetic inference places the UK populations amongst Central European samples. The combined datasets demonstrate that many of the UK populations can be treated as separate Management Units and we recommend that to preserve population specific genetic diversity, that stocking should be an intervention of last resort. However, if stocking is deemed essential, brood stock should originate from the river to be stocked.