Genomic diversity,population structure,and migration following rapid range expansion in the Balsam Poplar,Populus balsamifera

Rapid range expansions can cause pervasive changes in the genetic diversity and structure of populations. The postglacial history of the Balsam Poplar, Populus balsamifera, involved the colonization of most of northern North America, an area largely covered by continental ice sheets during the last glacial maximum. To characterize how this expansion shaped genomic diversity within and among populations, we developed 412 SNP markers that we assayed for a range‐wide sample of 474 individuals sampled from 34 populations. We complemented the SNP data set with DNA sequence data from 11 nuclear loci from 94 individuals, and used coalescent analyses to estimate historical population size, demographic growth, and patterns of migration. Bayesian clustering identified three geographically separated demes found in the Northern, Central, and Eastern portions of the species’ range. These demes varied significantly in nucleotide diversity, the abundance of private polymorphisms, and population substructure. Most measures supported the Central deme as descended from the primary refuge of diversity. Both SNPs and sequence data suggested recent population growth, and coalescent analyses of historical migration suggested a massive expansion from the Centre to the North and East. Collectively, these data demonstrate the strong influence that range expansions exert on genomic diversity, both within local populations and across the range. Our results suggest that an in‐depth knowledge of nucleotide diversity following expansion requires sampling within multiple populations, and highlight the utility of combining insights from different data types in population genomic studies.     

Allopatric divergence and regional range expansion of Juniperus sabina in China

In this study, we aimed to study the phylogeographic pattern of Juniperus sabina, a shrub species commonly occurring in the northern, northwestern and western China. We sequenced three chloroplast DNA fragments (trnL-trnF, trnS-trnG, and trriD-trriT) for 137 individuals from 16 populations of this species. Five chloroplast DNA chlorotypes (A, B, C, D, and E) were identified and they showed no overlapping distribution. The population subdivision is very high (GST = 0.926, NST= 0.980), suggesting a distinct phylogeographic structure (NST > GST, P < 0.05). Phylogenetic analyses of the five chlorotypes were clustered into three clades, consistent with their respective distributions in three separate regions: northern Xinjiang, western Xinjiang, and northern-northwestern China. However, within each region, the interpopulation differentiation is extremely low. These results as well as statistical tests suggested distinct allopatric differentiations between regional populations and independent glacial refugia for postglacial recolonization. The deserts that developed during the late Quaternary might have acted as effective barriers to promote genetic differentiation among these regions. However, the low diversity dominated by the single chlorotype within each fragmented region suggested that all current populations were derived from a common regional range expansion.     

Multiple lines of evidence for demographic and range expansion of a temperate species (Hyla sarda) during the last glaciation

Many temperate species experienced demographic and range contractions in response to climatic changes during Pleistocene glaciations. In this study, we investigate the evolutionary history of the Tyrrhenian tree frog Hyla sarda, a species inhabiting the Corsica-Sardinia island system (Western Mediterranean basin). We used sequence analysis of two mitochondrial (overall 1229 bp) and three nuclear (overall 1692 bp) gene fragments to assess the phylogeography and demographic history of this species, and species distribution modelling (SDM) to predict its range variation over time. Phylogeographic, historical demographic and SDM analyses consistently indicate that H. sarda does not conform to the scenario generally expected for temperate species but rather underwent demographic and range expansion mostly during the last glacial phase. Palaeogeographic data and SDM analyses suggest that such expansion was driven by the glaciation-induced increase in lowland areas during marine regression. This unusual scenario suggests that at least some temperate species may not have suffered the adverse effects of glacial climate on their population size and range extent, owing to the mitigating effects of other glaciations-induced palaeoenvironmental changes. We discuss previous clues for the occurrence of such a scenario in other species and some possible challenges with its identification. Early phylogeographic literature suggested that responses to the Pleistocene glacial-interglacial cycles were expected to vary among species and regions. Our results point out that such variation may have been greater than previously thought.     

Recency, range expansion, and unsorted lineages: implications for interpreting neutral genetic variation in the sharp-tailed grouse (Tympanuchus phasianellus)

Both current and historical patterns of variation are relevant to understanding and managing ecological diversity. Recently derived species present a challenge to the reconstruction of historical patterns because neutral molecular data for these taxa are more likely to exhibit effects of recent and ongoing demographic processes. We studied geographical patterns of neutral molecular variation in a species thought to be of relatively recent origin, Tympanuchus phasianellus (sharp-tailed grouse), using mitochondrial control region sequences (CR-I), amplified fragment length polymorphisms (AFLP), and microsatellites. For historical context, we also analysed CR-I in all species of Tympanuchus. Within T. phasianellus, we found evidence for restricted gene flow between eastern and western portions of the species range, generally corresponding with the range boundary of T. p. columbianus and T. p. jamesi. The mismatch distribution and molecular clock estimates from the CR-I data suggested that all Tympanuchus underwent a range expansion prior to sorting of mitotypes among the species, and that sorting may have been delayed as a result of mutation-drift disequilibrium. This study illustrates the challenge of using genetic data to detect historical divergence in groups that are of relatively recent origin, or that have a history dominated by nonequilibrium conditions. We suggest that in such cases, morphological, ecological, and behavioural data may be particularly important adjuncts to molecular data for the recognition of historically or adaptively divergent groups.     

Isolation by distance and post-glacial range expansion in the rough-skinned newt, Taricha granulosa

Allozymes and mitochondrial DNA sequences were used to examine the phylogeographical history of the rough-skinned newt, Taricha granulosa, in western North America. Nineteen populations were analysed for allozyme variation at 45 loci, and 23 populations were analysed for cytochrome b sequence variation. Both data sets agree that populations in the southern part of the range are characterized by isolation by distance, whereas northern populations fit the expectations of a recent range expansion. However, the northern limit of isolation by distance (and the southern limit of range expansion) is located in Oregon State by the mtDNA data, and in Washington State by the allozyme data. Nevertheless, both data sets are consistent with the known Pleistocene history of western North America, with phylogenetically basal populations in central and northern California, and a recent range expansion in the north following the retreat of the Cordilleran ice sheet 10,000 years ago. Additionally, a population in Idaho, previously considered introduced from central California based on morphometric analyses, possesses a distinct mtDNA haplotype, suggesting it could be native. The relevance of these results for Pacific Northwest biogeography is discussed.     

Eco‐genomic analysis of the poleward range expansion of the wasp spider Argiope bruennichi shows rapid adaptation and genomic admixture

Poleward range expansions are commonly attributed to global change, but could alternatively be driven by rapid evolutionary adaptation. A well‐documented example of a range expansion during the past decades is provided by the European wasp spider Argiope bruennichi. Using ecological niche modeling, thermal tolerance experiments and a genome‐wide analysis of gene expression divergence, we show that invasive populations have adapted to novel climatic conditions in the course of their expansion. Their climatic niche shift is mirrored in an increased cold tolerance and a population‐specific and functionally differentiated gene expression response. We generated an Argiope reference genome sequence and used population genome resequencing to assess genomic changes associated with the new climatic adaptations. We find clear genetic differentiation and a significant admixture with alleles from East Asian populations in the invasive Northern European populations. Population genetic modeling suggests that at least some of these introgressing alleles have contributed to the new adaptations during the expansion. Our results thus confirm the notion that range expansions are not a simple consequence of climate change, but are accompanied by fast genetic changes and adaptations that may be fuelled through admixture between long separated lineages.     

Inferring the mode of colonization of the rapid range expansion of a solitary bee from multilocus DNA sequence variation

Rapid geographic range expansions can have dramatic effects on the distribution of genetic diversity, both within and among populations. Based on field records collected over the past two decades in Western Europe, we report on the rapid geographic range expansion in Colletes hederae, a solitary bee species. To characterize how this expansion shaped the distribution of genetic diversity within and among populations, we performed a genetic analysis based on the sequencing of three nuclear loci (RNAp, CAD and WgL). We then simulated the evolution of DNA sequences under a spatially explicit model of coalescence to compare different hypotheses regarding the mode of colonization associated with this rapid expansion and to identify those that are most consistent with the observed molecular data. Our genetic analyses indicate that the range expansion was not associated with an important reduction in genetic diversity, even in the most recently colonized area in the United Kingdom. Moreover, little genetic differentiation was observed among populations. Our comparative analysis of simulated data sets indicates that the observed genetic data are more consistent with a demographic scenario involving relatively high migration rates than with a scenario based on a high reproduction rate associated with few migrants. In the light of these results, we discuss the factors that might have contributed to the rapid geographic range expansion of this pollen‐specialist solitary bee species across Western Europe.     

The social and ecological consequences of early cattle ranching in the Little Colorado River Basin

Commercial cattle ranching began in east central Arizona during the late 1880s when thousands of head of cattle were introduced onto the previously unexploited grasslands of the Little Colorado River Basin. Most of these animals were imported from western Texas where serious overgrazing had resulted in both catastrophic cattle losses and widespread range deterioration. By the turn of the century, the Texas experience had been repeated in Arizona, because Texas cattlemen continued to follow the same destructive stocking practices in this new region. This paper examines: (1) the early development of cattle ranching in the Little Colorado River Basin; (2) the various factors which contributed to overgrazing in the region; and (3) the consequences that commercial cattle ranching had on the local environment and on the pre-existing farming communities of the region.     

Northwestward range expansion of the bumblebee Bombus haematurus into Central Europe is associated with warmer winters and niche conservatism

Species range expansions are crucial for understanding niche formation and the interaction with the environment. Here, we studied the bumblebee Bombus haematurus Kriechbaumer, 1870, a species historically distributed from northern Serbia through northern Iran which has very recently started expanding northwestward into Central Europe without human-mediated dispersal (i.e., it is a natural spread). After updating the global distribution of this species, we investigated if niche shifts took place during this range expansion between newly colonized and historical areas. In addition, we have explored which climatic factors may have favored the natural range expansion of the species. Our results indicated that Bombus haematurus has colonized large territories in 7 European countries outside the historical area in the period from the 1980s to 2018, a natural expansion over an area that equals 20% of the historical distribution. In addition, this bumblebee performs generalism in flower visitation and it occurs in different habitats, although a preference for forested areas clearly emerges. The land-use associated with the species in the colonized areas is similar to the historical distribution, indicating that no major niche shifts occurred during the spread. Furthermore, in recently colonized localities, the range expansion was associated with warming temperatures during the winter and also during both queen overwintering and emergence phases. These findings document a case of natural range expansion due to environmental change rather than due to niche shifts, and specifically they suggest that warmer winters could be linked to the process of natural colonization of new areas.     

Recent postglacial range expansion drives the rapid diversification of a songbird lineage in the genus Junco

Pleistocene glacial cycles are thought to have played a major role in the diversification of temperate and boreal species of North American birds. Given that coalescence times between sister taxa typically range from 0.1 to 2.0 Myr, it has been assumed that diversification occurred as populations were isolated in refugia over long periods of time, probably spanning one to several full glacial cycles. In contrast, the rapid postglacial range expansions and recolonization of northern latitudes following glacial maxima have received less attention as potential promoters of speciation. Here we report a case of extremely rapid diversification in the songbird genus Junco as a result of a single continent-wide range expansion within the last 10 000 years. Molecular data from 264 juncos sampled throughout their range reveal that as the yellow-eyed junco (Junco phaeonotus) of Mesoamerica expanded northward following the last glacial maximum, it speciated into the dark-eyed junco (Junco hyemalis), which subsequently diversified itself into at least five markedly distinct and geographically structured morphotypes in the USA and Canada. Patterns of low genetic structure and diversity in mitochondrial DNA and amplified fragment length polymorphism loci found in dark-eyed juncos relative to Mesoamerican yellow-eyed juncos provide support for the hypothesis of an expansion from the south, followed by rapid diversification in the north. These results underscore the role of postglacial expansions in promoting diversification and speciation through a mechanism that represents an alternative to traditional modes of Pleistocene speciation.     

Recent and rapid population growth and range expansion of the Lyme disease tick vector,Ixodes scapularis,in North America

Migration is a primary force of biological evolution that alters allele frequencies and introduces novel genetic variants into populations. Recent migration has been proposed as the cause of the emergence of many infectious diseases, including those carried by blacklegged ticks in North America. Populations of blacklegged ticks have established and flourished in areas of North America previously thought to be devoid of this species. The recent discovery of these populations of blacklegged ticks may have resulted from either in situ growth of long‐established populations that were maintained at very low densities or by migration and colonization from established populations. These alternative evolutionary hypotheses were investigated using Bayesian phylogeographic approaches to infer the origin and migratory history of recently detected blacklegged tick populations in the Northeastern United States. The data and results indicate that newly detected tick populations are not the product of in situ population growth from a previously established population but from recent colonization resulting in a geographic range expansion. This expansion in the geographic range proceeded primarily through progressive and local migration events from southern populations to proximate northern locations although long‐distance migration events were also detected.     

Unravelling the effects of contemporary and historical range expansion on the distribution of genetic diversity in the damselfly Coenagrion scitulum

Although genetic diversity provides the basic substrate for evolution, there are a limited number of studies that assess the impact of recent climate change on intraspecific genetic variation. This study aims to unravel the degree to which historical and contemporary factors shape genetic diversity and structure across a large part of the range of the range‐expanding damselfly Coenagrion scitulum (Rambur, 1842). A total of 525 individuals from 31 populations were genotyped at nine microsatellites, and a subset was sequenced at two mitochondrial genes. We inferred the importance of geography, environmental factors, and recent range expansion on genetic diversity and structure. Genetic diversity decreased going westwards, suggesting a signature of historical post‐glacial expansion from east to west and the presence of eastern refugia. Although genetic differentiation decreased going northwards, it increased in the northern edge populations, suggesting a role of contemporary range expansion on the genetic make‐up of populations. The phylogeographical context was proven to be essential in understanding and identifying the genetic signatures of local contemporary processes. Within this framework, our results highlight that recent range expansion of a good disperser can decrease genetic diversity and increase genetic differentiation which should be considered when devising suitable conservation strategies.     

Out of the forest: past and present range expansion of a parthenogenetic weevil pest,or how to colonize the world successfully

Previous research revealed complex diversification patterns in the parthenogenetic weevil Naupactus cervinus. To understand the origin of clonal diversity and successful spreading of this weevil, we investigated its geographic origin and possible dispersal routes and whether parthenogens can persist in habitats under unsuitable environmental conditions. This study is based on samples taken throughout a broad area of the species’ range. We used both mitochondrial and nuclear markers and applied phylogenetic and network analyses to infer possible relationships between haplotypes. Bayesian phylogeographic analyses and ecological niche modeling were used to investigate the processes that shaped genetic diversity and enabled the colonization of new geographic areas. Southeastern Brazil emerges as the original distribution area of N. cervinus. We detected two range expansions, one along natural corridors during the Pleistocene and the other in countries outside South America during recent times. Isolation due to climate shifts during the early Pleistocene led to diversification in two divergent clades, which probably survived in different refugia of the Paranaense Forest and the Paraná River delta. The origin of the clonal diversity was probably a complex process including mutational diversification, hybridization, and secondary colonization. The establishment of N. cervinus in areas outside its native range may indicate adaptation to drier and cooler conditions. Parthenogenesis would be advantageous for the colonization of new environments by preventing the breakup of successful gene combinations. As in other insect pests, the present distribution of N. cervinus results from both its evolutionary history and its recent history related to human activities.     

Mitochondrial phylogeography of the European sprat (Sprattus sprattus L., Clupeidae) reveals isolated climatically vulnerable populations in the Mediterranean Sea and range expansion in the northeast Atlantic

We examined the genetic structure of the European sprat ( Sprattus sprattus ) by means of a 530-bp sequence of the mitochondrial control region from 210 fish originating from seven sampling localities of its distributional range. Phylogeographical analysis of 128 haplotypes showed a phylogenetic separation into two major clades with the Strait of Sicily acting as a barrier to gene flow between them. While no population differentiation was observed based on analysis of molecular variance and net nucleotide differences between samples of the Baltic Sea, the North Sea and the Bay of Biscay nor between the Black Sea and the Bosporus, a strong population differentiation between these samples and two samples from the Mediterranean Sea was found. Further, the biggest genetic distance was observed within the Mediterranean Sea between the populations of the Gulf of Lyon and the Adriatic Sea, indicating genetic isolation of these regions. Low genetic diversities and star-like haplotype networks of both Mediterranean Sea populations point towards recent demographic expansion scenarios after low population size, which is further supported by negative F _S values and unimodal mismatch distributions with a low mean. Along the northeast Atlantic coast, a northwards range expansion of a large and stable population can be assumed. The history of a diverse but differentiated Black Sea population remains unknown due to uncertainties in the palaeo-oceanography of this sea. Our genetic data did not confirm the presently used classification into subspecies but are only preliminary in the absence of nuclear genetic analyses.     

Inferring the geographic origin of a range expansion: Latitudinal and longitudinal coordinates inferred from genomic data in an ABC framework with the program x‐origin

Climatic or environmental change is not only driving distributional shifts in species today, but it has also caused distributions to expand and contract in the past. Inferences about the geographic locations of past populations especially regions that served as refugia (i.e., source populations) and migratory routes are a challenging endeavour. Refugial areas may be evidenced from fossil records or regions of temporal stability inferred from ecological niche models. Genomic data offer an alternative and broadly applicable source of information about the locality of refugial areas, especially relative to fossil data, which are either unavailable or incomplete for most species. Here, we present a pipeline we developed (called x ‐origin ) for statistically inferring the geographic origin of range expansion using a spatially explicit coalescent model and an approximate Bayesian computation testing framework. In addition to assessing the probability of specific latitudinal and longitudinal coordinates of refugial or source populations, such inferences can also be made accounting for the effects of temporal and spatial environmental heterogeneity, which may impact migration routes. We demonstrate x ‐origin with an analysis of genomic data collected in the Collared pika that underwent postglacial expansion across Alaska, as well as present an assessment of its accuracy under a known model of expansion to validate the approach.     

Quaternary range and demographic expansion of Liolaemus darwinii (Squamata: Liolaemidae) in the Monte Desert of Central Argentina using Bayesian phylogeography and ecological niche modelling

Until recently, most phylogeographic approaches have been unable to distinguish between demographic and range expansion processes, making it difficult to test for the possibility of range expansion without population growth and vice versa. In this study, we applied a Bayesian phylogeographic approach to reconstruct both demographic and range expansion in the lizard Liolaemus darwinii of the Monte Desert in Central Argentina, during the Late Quaternary. Based on analysis of 14 anonymous nuclear loci and the cytochrome b mitochondrial DNA gene, we detected signals of demographic expansion starting at ~55 ka based on Bayesian Skyline and Skyride Plots. In contrast, Bayesian relaxed models of spatial diffusion suggested that range expansion occurred only between ~95 and 55 ka, and more recently, diffusion rates were very low during demographic expansion. The possibility of population growth without substantial range expansion could account for the shared patterns of demographic expansion during the Last Glacial Maxima (OIS 2 and 4) in fish, small mammals and other lizards of the Monte Desert. We found substantial variation in diffusion rates over time, and very high rates during the range expansion phase, consistent with a rapidly advancing expansion front towards the southeast shown by palaeo‐distribution models. Furthermore, the estimated diffusion rates are congruent with observed dispersal rates of lizards in field conditions and therefore provide additional confidence to the temporal scale of inferred phylogeographic patterns. Our study highlights how the integration of phylogeography with palaeo‐distribution models can shed light on both demographic and range expansion processes and their potential causes.     

Dispersal strategies, secondary range expansion and invasion genetics of the nonindigenous round goby, Neogobius melanostomus, in Great Lakes tributaries

Dispersal strategies are important mechanisms underlying the spatial distribution and colonizing ability of all mobile species. In the current study, we use highly polymorphic microsatellite markers to evaluate local dispersal and colonization dynamics of the round goby (Neogobius melanostomus), an aquatic invader expanding its range from lake to river environments in its introduced North American range. Genetic structure, genotype assignment and genetic diversity were compared among 1262 round gobies from 20 river and four lake sites in three Great Lakes tributaries. Our results indicate that a combination of short-distance diffusion and long-distance dispersal, collectively referred to as 'stratified dispersal', is facilitating river colonization. Colonization proceeded upstream yearly (approximately 500 m/year; 2005-2009) in one of two temporal replicates while genetic structure was temporally stable. Contiguous dispersal from the lake was observed in all three rivers with a substantial portion of river fish (7.3%) identified as migrants. Genotype assignment indicated a separate introduction occurred upstream of the invasion front in one river. Genetic diversity was similar and relatively high among lake and recently colonized river populations, indicating that founder effects are mitigated through a dual-dispersal strategy. The remarkable success of round goby as an aquatic invader stresses the need for better diffusion models of secondary range expansion for presumably sessile invasive species.