Mitochondrial DNA haplotypes indicate two postglacial re‐colonization routes of the spruce bark beetle Ips typographus through northern Europe to Scandinavia

Species in northern Europe re‐colonized the region after the last glacial maximum via several routes, which could have lingering signatures in current intraspecific trait variation. The spruce bark beetle, Ips typographus, occurs across Europe, and biological differences have been found between southern and northern Scandinavian populations. However, the postglacial history of I. typographus in Scandinavia has not been previously studied at a fine geographical scale. Therefore, we collected specimens across northern Europe and analysed the genetic variation in a quite large mitochondrial fragment (698 bp). A high genetic diversity was found in some of the most northern populations, in the Baltic States, Gotland and central Europe. Detected genetic and phylogeographic structures suggest that I. typographus re‐colonized Scandinavia via two pathways, one from the northeast and one from the south. These findings are consistent with the re‐colonization history of its host plant, Picea abies. However, we observed low haplotype and nucleotide diversity in southern Scandinavian populations of I. typographus, indicating that (unlike P. abies) it did not disperse across the Baltic Sea in multiple events. Further, the divergence among Scandinavian populations was shallow, conflicting with a scenario where I. typographus expanded concurrently with its host plant from a ‘cryptic refugium’ in the northwest.     

Performance of the tree‐killing bark beetles Ips typographus and Pityogenes chalcographus in non‐indigenous lodgepole pine and their historical host Norway spruce

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Comparative multilocus phylogeography of two Palaearctic spruce bark beetles: influence of contrasting ecological strategies on genetic variation

While phylogeographic patterns of organisms are often interpreted through past environmental disturbances, mediated by climate changes, and geographic barriers, they may also be strongly influenced by species‐specific traits. To investigate the impact of such traits, we focused on two Eurasian spruce bark beetles that share a similar geographic distribution, but differ in their ecology and reproduction. Ips typographus is an aggressive tree‐killing species characterized by strong dispersal, whereas Dendroctonus micans is a discrete inbreeding species (sib mating is the rule), parasite of living trees and a poor disperser. We compared genetic variation between the two species over both beetles’ entire range in Eurasia with five independent gene fragments, to evaluate whether their intrinsic differences could have an influence over their phylogeographic patterns. We highlighted widely divergent patterns of genetic variation for the two species and argue that the difference is indeed largely compatible with their contrasting dispersal strategies and modes of reproduction. In addition, genetic structure in I. typographus divides European populations in a northern and a southern group, as was previously observed for its host plant, and suggests past allopatric divergence. A long divergence time was estimated between East Asian and other populations of both species, indicating their long‐standing presence in Eurasia, prior to the last glacial maximum. Finally, the strong population structure observed in D. micans for the mitochondrial locus provides insights into the recent colonization history of this species, from its native European range to regions where it was recently introduced.     

Characterization of microsatellite loci in the spruce bark beetle Ips typographus (Coleoptera: Scolytinae)

Ips typographus is an economically important pest of Norway spruce stands. We developed five polymorphic microsatellite markers using a biotin enrichment protocol. The number of alleles ranged from three to 11 per locus and no strong evidence for null alleles was found. Heterozygosity ranged from 0.3 to 0.97. These markers could be useful tools to study the population structure and genetic consequences of I. typographus population outbreaks.     

Monitoring of Ips typographus and Pityogenes chalcographus: influence of trapping site and surrounding landscape on catches

• 1 The influence of trapping site (i.e. fresh clear‐cuts) characteristics and habitat amount (i.e. area of stands that may hold breeding material) in the surrounding landscape on catches of the bark beetles Ips typographus (L.) and Pityogenes chalcographus (L.) in pheromone‐baited flight‐barrier monitoring traps was studied.
• 2 For the two species, the study investigated: (i) the extent of the variation in catches among trapping sites; (ii) the extent of this variation that can be explained by models including trapping site characteristics (clear‐cut size, percentage of spruce in the cut stand, altitude) and habitat amounts in the surrounding landscape; and (iii) the spatial scale at which beetles respond to the habitat amount in the landscape.
• 3 The variation in catches among trap sites was 15‐fold larger for I. typographus than for P. chalcographus. There was a positive relationship between the catches of I. typographus and (i) the percentage of the surrounding landscape covered by mature spruce forest at radii 500–4000 m and (ii) the percentage of spruce in stands cut when the clear‐cuts used as trapping sites were created. For P. chalcographus, only the second relationship could be demonstrated.
• 4 Thus, for monitoring of I. typographus: (i) several trapping sites per landscape are required; (ii) the amount of mature spruce forest around trapping sites needs to be considered when choosing trapping sites; and (iii) the trapping sites need to be standardized with respect to the percentage of spruce in the cut stand when fresh clear‐cuts are used. For P. chalcographus, fewer trapping sites per landscape are required and only the percentage of spruce in the cut stand needs to be considered.

     

Pathogens of Ips amitinus: new species and comparison with Ips typographus

Ips amitinus and I. typographus are two serious pests of spruce in Europe, have similar bionomics and are likely to occur and meet on the same host trees. We therefore hypothesized that the two species support similar levels of similar pathogens. To test this hypothesis, we collected mature beetles from three trap trees at each of eight study sites and determined beetle numbers and pathogen infection levels. In total, 938 mature I. amitinus beetles and 3435 of I. typographus were dissected; five pathogens, as well as intestinal nematodes and endoparasitoids, were detected. The neogregarine Mattesia schwenkei is reported here for the first time as a new pathogen in 9.4% of I. amitinus individuals at one site. Average infection levels of most pathogens (Chytridiopsis typographi, Gregarina typographi, Mattesia schwenkei and parasitoids) were significantly higher in I. typographus than in I. amitinus. Metschnikowia typographi was confirmed only in Ips amitinus, while the microsporidium of Nosema typographi occurred only in I. typographus. Within‐season increases in G. typographi infection levels were documented in Ips amitinus.     

Occurrence of pathogens in Ips typographus (Coleoptera: Curculionidae) and in other spruce bark beetles from the wilderness reserve Dürrenstein (Lower Austria)

The study presents new data on spatial distribution of bark beetle pathogens, on changes in frequency over several years and on their prevalence during different time periods within a year from several locations within the wilderness reserve Dürrenstein (Lower Austria). The occurrence of pathogens was investigated in Ips typographus (during five years), in Pityogenes chalcographus (during two years) and in Ips amitinus (in one year). In total, seven pathogen species could be detected in I. typographus. The most dominant pathogen species were the Ips typographus-Entomopoxvirus (ItEPV), the sporozoan species Gregarina typographi and the microsporidium Chytridiopsis typographi; the latter two pathogen species were recorded every year and at about similar high (G. typographi) or low (C. typographi) rates, the ItEPV in strongly varying rates. The neogregarine Mattesia cf. schwenkei and the two microsporidia Nosema typographi and Unikaryon montanum were found in I. typographus only sporadically and the rhizopodan species Malamoeba scolyti was found once. The number of infected males and females was relatively similar with almost all pathogen species in most of the years except U. montanum, which occurred exclusively in females. Three pathogen species were recorded in P. chalcographus which were Gregarina typographi, Mattesia cf. schwenkei and Chytridiopsis typographi. Two pathogen species were observed in I. amitinus, Gregarina typographi and Chytridiopsis typographi.     

Spatial genetic structure in Beta vulgaris subsp. maritima and Beta macrocarpa reveals the effect of contrasting mating system,influence of marine currents,and footprints of postglacial recolonization routes

Understanding the factors that contribute to population genetic divergence across a species' range is a long‐standing goal in evolutionary biology and ecological genetics. We examined the relative importance of historical and ecological features in shaping the present‐day spatial patterns of genetic structure in two related plant species, Beta vulgaris subsp. maritima and Beta macrocarpa. Using nuclear and mitochondrial markers, we surveyed 93 populations from Brittany (France) to Morocco – the southern limit of their species' range distribution. Whereas B. macrocarpa showed a genotypic structure and a high level of genetic differentiation indicative of selfing, the population genetic structure of B. vulgaris subsp. maritima was consistent with an outcrossing mating system. We further showed (1) a strong geographic clustering in coastal B. vulgaris subsp. maritima populations that highlighted the influence of marine currents in shaping different lineages and (2) a peculiar genetic structure of inland B. vulgaris subsp. maritima populations that could indicate the admixture of distinct evolutionary lineages and recent expansions associated with anthropogenic disturbances. Spatial patterns of nuclear diversity and differentiation also supported a stepwise recolonization of Europe from Atlantic‐Mediterranean refugia after the last glacial period, with leading‐edge expansions. However, cytoplasmic diversity was not impacted by postglacial recolonization: stochastic long‐distance seed dispersal mediated by major oceanic currents may mitigate the common patterns of reduced cytoplasmic diversity observed for edge populations. Overall, the patterns we documented here challenge the general view of reduced genetic diversity at the edge of a species' range distribution and provide clues for understanding how life‐history and major geographic features interact to shape the distribution of genetic diversity.     

Phylogeography of the Alcippe morrisonia (Aves: Timaliidae): long population history beyond late Pleistocene glaciations

Background  

The role of Pleistocene glacial oscillations in current biodiversity and distribution patterns varies with latitude, physical topology and population life history and has long been a topic of discussion. However, there had been little phylogeographical research in south China, where the geophysical complexity is associated with great biodiversity. A bird endemic in Southeast Asia, the Grey-cheeked Fulvetta, Alcippe morrisonia, has been reported to show deep genetic divergences among its seven subspecies. In the present study, we investigated the phylogeography of A. morrisonia to explore its population structure and evolutionary history, in order to gain insight into the effect of geological events on the speciation and diversity of birds endemic in south China.     

Genetic divergence of Chilean long‐tailed snake (Philodryas chamissonis) across latitudes: conservation threats for different lineages

Aim The Chilean long‐tailed snake (Philodryas chamissonis) has a wide distribution across different latitudes and ecosystems in Chile ranging from the south of the Atacama Desert (26° S) to the extremely humid Valdivian temperate rain forest (40° S). Throughout this vast distribution, which is isolated by the Andes mountain range on the east and the Pacific Ocean on the west, there are biogeographical boundaries and large geographical barriers that must have played an important role in the distribution of genetic diversity within this species. This study aimed at elucidating the evolutionary history of P. chamissonis in Chile by analysis of mitochondrial DNA sequences. Location Chile (29°41′–38°23′ S). Methods We extracted DNA from 66 tissue samples collected across different latitudes and amplified and sequenced the mitochondrial DNA control region and the NADH dehydrogenase subunit 4 gene for phylogenetic and population analysis. Results Four distinct haplogroups were identified for P. chamissonis. These are highly consistent with a latitudinal geographic pattern, different ecosystems and the increase in topography towards central Chile. Three of the four haplogroups are concentrated in central Chile (33° S latitude) where the highest herpetofaunal diversity of the country is found. The Maipo River acts as historical geographical barrier for the species influenced by Pleistocene glaciation cycles, leading to a marked phylogeographical boundary. A strong population structure was found for the species (Φ_st = 0.78, P < 0.0001), with a high haplotype diversity (h = 0.97 ± 0.01) and nucleotide diversity (π = 0.0151 ± 0.0077). Main conclusions At least three evolutionarily significant units (ESUs) were designated for the species, and these should be taken into account for conservation plans. Three of the four haplogroups found within P. chamissonis are already threatened because their distribution along central Chile overlaps with most of the largest cities in the country.     

Zur Schwermetallbelastung der Borkenkäfer

Zusammenfassung Es wurde der Schwermetallgehalt (Cd, Mn, Pb, Zn) de für die Ernährung von Borkenkäfern relevanten Gewebe an Fichten (Picea abies Karst.) unterschiedlicher Standorte untersucht sowie dessen Auswirkung auf den Metallgehalt der dort minierenden Käfer (Ips typographus L.,Pityogenes chalcographus L. undPolygraphus poligraphus L., - Scolytidae) ermittelt. Für Cadmium und Zink konnte eine deutliche Anreicherung in den Käfern sowie eine entsprechende Abhängigkeit von der Konzentration im Futter nachgewiesen werden. Der Bast von Fichten weist teilweise sehr hohe Mangankonzentrationen und eine sehr breite Streuung auf. Die in diesem Bast entwickelten Käfer zeigen dagegen einheitlich niedrige Konzentrationen (unsicher beiI. typographus). Die Bleikonzentrationen waren in den Käferproben geringfügig höher als in den Bastproben, eine Abhängigkeit der Konzentrationen in Käfer und Bast wurde im untersuchten Konzentrationsbereich jedoch nicht gefunden. Die verschiedenen Entwicklungsstadien der Käfer wurden ebenfalls vergleichend auf ihren Schwermetallgehalt hin untersucht.

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Heavy metal contamination of bark beetles

Summary Heavy metal concentrations (cadmium, lead, manganese, zinc) in bark and wood of the sprucePicea abies Karst. from different locations were determined by AAS-method and compared with that of the bark-beetles feeding on it (Ips typographus L.,Pityogenes chalcographus L.,Polygraphus poligraphus L. — Scolytidae).In the case of cadmium and zinc a positive correlation of metal concentration in beetles and food as well as an accumulation in the beetles could be shown. We found considerable variation of manganese content (up to a factor of 100) in the inner bark (the main feeding substrate of the animals) but relatively uniform concentration in the insects (uncertain in the case ofI. typographus). Mean lead concentrations were slightly higher in beetles than in food, but no correlation between the insects and their feeding substrate could be detected in the range investigated. The heavy metal concentrations of different stages of development are compared and a short-circuit Cd-excretion mechanism in the larval stage is discussed.

     

Gene flow from multiple sources maintains high genetic diversity and stable population history of Common Moorhen Gallinula chloropus in China

In this study, we used mitochondrial control sequences and microsatellite data from 231 Common Moorhen Gallinula chloropus individuals sampled from 19 sites in China to analyse their genetic structure and evolutionary history. High genetic diversity was found for all populations, although microsatellite analysis showed that the genetic diversity in non‐migratory populations was significantly higher than in migratory populations. High gene flow occurred between neighbouring populations, although long‐distance gene flow also occurred. The Huazhong population was the single greatest genetic source for other populations. High gene flow probably led to the shallow genetic structure that we observed. Demographic expansion was found in migratory populations, non‐migratory populations and with all individuals combined. The expansion time for all populations combined was estimated to be 221 000 years ago. The Common Moorhen population grew rapidly during the interglacial before the last glacial maximum (LGM), then remained generally stable from the LGM to the present.     

New insights into the evolutionary history of Plasmodium falciparum from mitochondrial genome sequence analyses of Indian isolates

Estimating genetic diversity and inferring the evolutionary history of Plasmodium falciparum could be helpful in understanding origin and spread of virulent and drug‐resistant forms of the malaria pathogen and therefore contribute to malaria control programme. Genetic diversity of the whole mitochondrial (mt) genome of P. falciparum sampled across the major distribution ranges had been reported, but no Indian P. falciparum isolate had been analysed so far, even though India is highly endemic to P. falciparum malaria. We have sequenced the whole mt genome of 44 Indian field isolates and utilized published data set of 96 genome sequences to present global genetic diversity and to revisit the evolutionary history of P. falciparum. Indian P. falciparum presents high genetic diversity with several characteristics of ancestral populations and shares many of the genetic features with African and to some extent Papua New Guinean (PNG) isolates. Similar to African isolates, Indian P. falciparum populations have maintained high effective population size and undergone rapid expansion in the past with oldest time to the most recent common ancestor (TMRCA). Interestingly, one of the four single nucleotide polymorphisms (SNPs) that differentiates P. falciparum from P. falciparum‐like isolates (infecting non‐human primates in Africa) was found to be segregating in five Indian P. falciparum isolates. This SNP was in tight linkage with other two novel SNPs that were found exclusively in these five Indian isolates. The results on the mt genome sequence analyses of Indian isolates on the whole add to the current understanding on the evolutionary history of P. falciparum.     

Size and shape changes of Ips typographus L. (Coleoptera: Scolytinae) in relation to population level

1 High intraspecific competition is known to occur during Ips typographus outbreaks, and is thought to be the main factor regulating epidemic populations by affecting beetle population productivity. However, little is known about the consequences of intraspecific competition on population quality during outbreaks, although it could have consequences on beetle population dynamics. 2 Ips typographus morphological variations among localities, years and beetle population levels were investigated in 10 Norway spruce (Picea abies) stands having various beetle damage intensities. Beetle size and shape estimators based on wing length, and using isometric size and log‐shape ratios, were employed. Field‐caught beetles were compared with beetles emerging from controlled breeding at different densities, performed in the laboratory. Beetles from this colony were also used to check the influence of breeding densities on the size estimator. 3 Size variations occurred among localities and years and were consistent with the epidemic or latent status of the beetle populations. Controlled breeding confirmed the negative effect of beetle densities encountered in the field on offspring size. Two hypotheses are formulated to explain this increase of intraspecific competition during an outbreak, but our data support the effect of host quality change between latent and epidemic populations. 4 Shape variations also occurred among localities but were unrelated to beetle population levels. No groups consistent with a geographical structure were found, suggesting low genetic variation for I. typographus populations in France.     

Determining population structure and hybridization for two iris species

Identifying processes that promote or limit gene flow can help define the ecological and evolutionary history of a species. Furthermore, defining those factors that make up “species boundaries” can provide a definition of the independent evolutionary trajectories of related taxa. For many species, the historic processes that account for their distribution of genetic variation remain unresolved. In this study, we examine the geographic distribution of genetic diversity for two species of Louisiana Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how populations are structured and if population structure coincides with potential barriers to gene flow. We also asked whether there is evidence of hybridization between these two species outside Louisiana hybrid zones. We used a genotyping‐by‐sequencing approach and sampled a large number of single nucleotide polymorphisms across these species' genomes. Two different population assignment methods were used to resolve population structure in I. brevicaulis; however, there was considerably less population structure in I. fulva. We used a species tree approach to infer phylogenies both within and between populations and species. For I. brevicaulis, the geography of the collection locality was reflected in the phylogeny. The I. fulva phylogeny reflected much less structure than detected for I. brevicaulis. Lastly, combining both species into a phylogenetic analysis resolved two of six populations of I. brevicaulis that shared alleles with I. fulva. Taken together, our results suggest major differences in the level and pattern of connectivity among populations of these two Louisiana Iris species.     

Microsatellite and mtDNA analysis of lake trout,Salvelinus namaycush,from Great Bear Lake,Northwest Territories: impacts of historical and contemporary evolutionary forces on Arctic ecosystems

Resolving the genetic population structure of species inhabiting pristine, high latitude ecosystems can provide novel insights into the post‐glacial, evolutionary processes shaping the distribution of contemporary genetic variation. In this study, we assayed genetic variation in lake trout (Salvelinus namaycush) from Great Bear Lake (GBL), NT and one population outside of this lake (Sandy Lake, NT) at 11 microsatellite loci and the mtDNA control region (d‐loop). Overall, population subdivision was low, but significant (global F_ST θ = 0.025), and pairwise comparisons indicated that significance was heavily influenced by comparisons between GBL localities and Sandy Lake. Our data indicate that there is no obvious genetic structure among the various basins within GBL (global F_ST = 0.002) despite the large geographic distances between sampling areas. We found evidence of low levels of contemporary gene flow among arms within GBL, but not between Sandy Lake and GBL. Coalescent analyses suggested that some historical gene flow occurred among arms within GBL and between GBL and Sandy Lake. It appears, therefore, that contemporary (ongoing dispersal and gene flow) and historical (historical gene flow and large founding and present‐day effective population sizes) factors contribute to the lack of neutral genetic structure in GBL. Overall, our results illustrate the importance of history (e.g., post‐glacial colonization) and contemporary dispersal ecology in shaping genetic population structure of Arctic faunas and provide a better understanding of the evolutionary ecology of long‐lived salmonids in pristine, interconnected habitats.     

Comprehensive analysis of the mitochondrial DNA diversity in Chinese cattle

Complete mitochondrial DNA D‐loop sequences of 1105 individuals were used to assess the diversity of maternal lineages of cattle populations in China. In total, 250 taurine and 88 zebu haplotypes were identified. Five main haplogroups—T1a, T2, T3, T4 and T5—were identified in Bos taurus, whereas Bos indicus harbored two haplogroups—I1 and I2. Our results suggest that the distribution of T1a in Asia was concentrated mainly in the northeast region (northeast China, Korea and Japan); haplogroups T2, T3 and T4 were predominant in Chinese cattle; and T5 was sporadically detected in Mongolian and Pingwu cattle. In contrast to the widespread presence of I1, I2 was distributed only in southwestern China (Yunnan‐Guizhou Plateau and the Tibet Autonomous Region) and Xinjiang Uygur Autonomous Region. This is the first time that all five taurine haplogroups and two zebu haplogroups have been found in Mongolian cattle. In addition, eight individuals in Tibetan cattle carried the Bos grunniens mtDNA type. The high mtDNA diversity (H = 0.904 ± 0.008) and the weak genetic structure among the 57 Chinese cattle breeds/populations are consistent with their complex historical background, migration route and ecological environment.     

Mitochondrial DNA variation of Nigerian domestic helmeted guinea fowl

We analyzed genetic diversity of 215 mitochondrial DNA (mtDNA) D‐loop sequences from seven populations of domesticated helmeted guinea fowl (Numida meleagris) in Nigeria and compared that with results of samples collected in Kenya (n = 4) and China (n = 22). In total, 241 sequences were assigned to 22 distinct haplotypes. Haplotype diversity in Nigeria was 0.693 ± 0.022. The network grouped most matrilines into two main haplogroups: A and B. There was an absence of a geographic signal, and two haplotypes dominated across all locations with the exception of the Kebbi population in the northwest of the country; AMOVA also confirmed this observation (F_ST = 0.035). The low genetic diversity may be a result of recent domestication, whereas the lack of maternal genetic structure likely suggests the extensive genetic intermixing within the country. Additionally, the differentiation of the Kebbi population may be due to a certain demographic history and/or artificial selection that shaped its haplotype profile. The current data do not permit us to make further conclusions; therefore, more research evidence from genetics and archaeology is still required.     

Effects of heat on the dispersal performance of Ips typographus

Under present climate conditions, Ips typographus (L.) is Europe's most critical disturbance agent for mature Norway spruce (Picea abies). With ongoing climate change, the bark beetle will most probably become more prominent as a pest. The aim of this study was to analyse the dispersal performance of I. typographus under various weather conditions, especially hot days with a maximum air temperature above 30°C. In a field study, marked bark beetles were released from breeding logs and could be retraced in traps distributed across the survey area. With daily collections of the trapped beetles, it was possible to analyse the flight activity and the average flight distance of the bark beetles during hot, moderate and cool days. The numbers of daily catches and the average flight distance during the hottest days (air temperature maximum ≥30°C) did not significantly differ from the moderate days (air temperature maximum ≥22°C and <30°C). The numbers of daily catches and the average flight distance during the cool days (air temperature maximum <22°C) were significantly lower than during hot and moderate days. The results give an insight on the dispersal capacity of I. typographus under climate change driven future conditions. Increased air temperatures do not seem to impair the flight performance of I. typographus. A small proportion of cool days during the swarming period even seems to favour dispersal of I. typographus.     

Postglacial range shift and demographic expansion of the marine intertidal snail Batillaria attramentaria

To address the impacts of past climate changes, particularly since the last glacial period, on the history of the distribution and demography of marine species, we investigated the evolutionary and demographic responses of the intertidal batillariid gastropod, Batillaria attramentaria, to these changes, using the snail as a model species in the northwest Pacific. We applied phylogeographic and divergence population genetic approaches to mitochondrial COI sequences from B. attramentaria. To cover much of its distributional range, 197 individuals collected throughout Korea and 507 publically available sequences (mostly from Japan) were used. Finally, a Bayesian skyline plot (BSP) method was applied to reconstruct the demographic history of this species. We found four differentiated geographic groups around Korea, confirming the presence of two distinct, geographically subdivided haplogroups on the Japanese coastlines along the bifurcated routes of the warm Tsushima and Kuroshio Currents. These two haplogroups were estimated to have begun to split approximately 400,000 years ago. Population divergence analysis supported the hypothesis that the Yellow Sea was populated by a northward range expansion of a small fraction of founders that split from a southern ancestral population since the last glacial maximum (LGM: 26,000–19,000 years ago), when the southern area became re‐submerged. BSP analyses on six geographically and genetically defined groups in Korea and Japan consistently demonstrated that each group has exponentially increased approximately since the LGM. This study resolved the phylogeography of B. attramentaria as a series of events connected over space and time; while paleoceanographic conditions determining the connectivity of neighboring seas in East Asia are responsible for the vicariance of this species, the postglacial sea‐level rise and warming temperatures have played a crucial role in rapid range shifts and broad demographic expansions of its populations.