Colonized North America Research Articles

Molecular phylogenetics and biogeography reveal the origin of cherries (Prunus subg. Cerasus, Rosaceae)

Abstract Cherries (subg. Cerasus) belong to Prunus s.l. (Rosaceae) and are widely distributed in temperate and subtropical regions of the Northern Hemisphere. Given its ornamental and edible functions, it is a hugely preferred germplasm resource for human societies. However, the interspecific phylogenetic relationships, divergence times, and routes of this subgenus remain unclear. To reveal its enigmatic and intricate evolutionary history, we newly sequenced 12 subg. Cerasus species, reconstructed the plastome phylogeny with 24 previously published subg. Cerasus species. This study supports that subg. Cerasus split into five clades, among which P. mahaleb is the basal group of subg. Cerasus; P. campanulata is genetically distantly related to P. cerasoides and is not recommended for treatment as a variety of the latter; P. subhirtella is involved in the speciation of P. yedoensis. Molecular dating and ancestral area reconstructions infer that subg. Cerasus originated in the Eastern Mediterranean–Central Asia before 11.57 Mya (95% HPD = 5.34–19.1 Mya) and subsequently spread into the Qinghai-Tibetan Plateau (QTP) and adjacent regions. The first dispersal event of modern subg. Cerasus was facilitated by ‘out-of-QTP’, colonizing North America across the Bering Land Bridge and re-dispersing into Europe from the Late Miocene to Pliocene and forming the initial distribution pattern of extant subg. Cerasus in the Pliocene; The end of the Quaternary glacial period witnessed a second dispersal event, and core subg. Cerasus population diversity flourished radially in its separate refugia during the Late Pleistocene.

Tracing the dispersal route of the invasive Japanese beetle Popillia japonica

The Japanese beetle, Popillia japonica, is a highly polyphagous Scarabaeidae native to Japan that colonized North America and Azores in the last century and has recently invaded Italy and Switzerland. Considering its economic impact on the horticulture and turfgrass industries, this species was ranked within the EU priority pests list in 2019. According to the EU Convention on Biological Diversity, the identification of invasion routes is a pivotal aspect in an effective management program aimed at controlling invasive alien species. To reconstruct the source of introductions of this pest, we investigated the genetic variability of P. japonica in its native and invaded areas worldwide by analyzing 9 microsatellite loci and two mitochondrial genes, COX I and CytB. In its native area, P. japonica is structured into two populations: one in the southern and another in the northern-central region of Japan. A limited area within central Japan was identified as the putative source of the North American outbreak. Moreover, the ABC inference and phylogeographic reconstruction suggest that two European populations originated from two independent introductions. The Azores Islands outbreak occurred approximately 50 years ago and originated from the southeastern region of North America (For simplicity, in this paper North America refers to Canada and the USA), while the second introduction, more recently, occurred in Italy and Switzerland and originated from northeastern region of North America.

Late Cenozoic history and the role of Beringia in assembling a Holarctic cestode species complex

The dynamic climate history that drove sea level fluctuation during past glacial periods mediated the movement of organisms between Asia and North America via the Bering Land Bridge. Investigations of the biogeographic histories of small mammals and their parasites demonstrate facets of a complex history of episodic geographic colonization and refugial isolation that structured diversity across the Holarctic. We use a large multi-locus nuclear DNA sequence dataset to robustly resolve relationships within the cestode genus Arostrilepis (Cyclophyllidea: Hymenolepididae), a widespread parasite of predominantly arvicoline rodents (voles, lemmings). Using this phylogeny, we confirm that several Asian Arostrilepis lineages colonized North America during up to four distinct glacial periods in association with different rodent hosts, consistent with taxon-pulse dynamics. A previously inferred westward dispersal across the land bridge is rejected. We also refine interpretations of past host colonization, providing evidence for several distinct episodes of expanding host range, which probably contributed to diversification by Arostrilepis. Finally, Arostrilepis is shown to be paraphyletic with respect to Hymenandrya thomomyis, a parasite of pocket gophers, confirming that ancient Arostrilepis species colonized new host lineages upon arriving in North America.

Evolutionary legacy of the extirpated red wolf clings to life in gulf-coast canids.

Before Europeans colonized North America, a uniquely American wolf roamed the eastern forests of southern Canada to Florida and west to the Great Plains. Known today as "red wolf" (Canis rufus) in the south and "eastern wolf" (Canis lycaon) in the north, evidence suggests that these indigenous forest wolves shared a common evolutionary history until only a few centuries ago when they were extirpated from the intervening majority of their historical range. While the eastern wolf persists today primarily as a small population in Algonquin Provincial Park, Canada, the red wolf was ostensibly driven from its last stronghold in gulf-coastal Louisiana and Texas by 1980. The last-known red wolves were taken captive for propagation and reintroduction. Today, the red wolf exists as ~250 descendants of 12 founders and are distributed among 42 captive breeding facilities and one reintroduced population in coastal North Carolina. As red and eastern wolves declined in the 20th century, coyotes expanded from the west into the eastern forests, replacing them. Along with human persecution, coyote hybridization has been blamed for the late 20th century demise of the red wolf. However, rather than helping to drive the red wolf to extinction, coyote hybridization may have instead helped to preserve it. In this issue of Molecular Ecology, vonHoldt and colleagues provide the most comprehensive description yet of the substantial quantity and distribution of red wolf ancestry sequestered in southeastern coyote populations. They find the highest frequency of red wolf genes in coyotes from the gulf-coastal sites where the last known wild red wolves occurred, but also present evidence for a high prevalence of red wolf genes in coyotes throughout the southeastern expansion zone. Given the significant reduction in genetic diversity in extant red wolves owing to their late 20th century population bottleneck, this coyote-sequestered reservoir of red wolf genes could prove an important resource for red wolf conservation.

Genetic Structure and Colonization of North America by Depressaria depressana (Fabricius 1775) (Lepidoptera: Depressariidae) over 15 Years; Contrasts with Westward Expansion of Depressaria radiella (Goeze, 1783) over 160 Years.

Simple SummaryAs invasive insect species can disrupt agriculture, ecosystem functions, and human health, monitoring the spread of newly invasive insects is a high priority. The purple carrot-seed moth Depressaria depressana, a European species first reported in North America in 2008, specializes on reproductive structures of taxa throughout the family Apiaceae and thus presents a potential threat to native North American umbellifers. We assessed interpopulational genetic diversity of D. depressana across its eastern North American invasion front and compared those values to available data for European populations. We also compared this diversity with genetic diversity estimates for populations of Depressaria radiella (parsnip webworm), a European species introduced to North America more than 160 years ago that is essentially restricted to two apiaceous genera throughout its native and invasive ranges. Documenting the historical spread of D. radiella with museum and literature records, we found D. depressana displays greater genetic diversity than D. radiella and is colonizing North America more rapidly; greater genetic diversity may facilitate faster colonization via establishment on a wider range of hostplants. The contrast in colonization by these two species may inform management practices for invasive insects utilizing a broad versus narrow array of hosts within a single plant family.Depressaria depressana, the purple carrot seed moth, is a Eurasian species first reported in North America in 2008 and currently undergoing range expansion. This invasion follows that of its Eurasion congener Depressaria radiella (parsnip webworm), first documented in North America 160 years ago. Unlike D. depressana, which utilizes hostplants across multiple tribes of Apiaceae, Depressaria radiella is a “superspecialist” effectively restricted in its native and non-indigenous ranges to two closely related apiaceous genera. We investigated the genetic structure of D. depressana populations across latitudinal and longitudinal gradients in the eastern United States by constructing COI haplotype networks and then comparing these with haplotype networks constructed from available COI sequence data from contemporary European D. depressana populations and from European and North American D. radiella populations. Haplotype data revealed higher genetic diversity in D. depressana, indicating high dispersal capacity, multiple introductions, and/or a genetically diverse founding population. Museum and literature records of D. radiella date back to 1862 and indicate that range expansion to the West Coast required more than 50 years. Higher levels of genetic diversity observed in D. depressana compared to its congener may indicate a greater propensity for dispersal, colonization and establishment in its non-indigenous range.

Prehistoric perspectives can help interpret the present: 14 000 years of moose (Alces alces) in the Western Arctic

Rapidly changing climate at high latitudes has triggered a search for bellwethers of ecological change there. If the initial signs of change can be identified, perhaps we can predict where these changes will lead. Large-bodied, terrestrial herbivores are potential candidates for bellwether taxa because of the key roles they play in some ecological communities. Here, we assembled historical, archaeological, and paleontological records of moose ( Alces alces (Linnaeus, 1758)) from the western Arctic and subarctic. The results showed that rather than having recently invaded tundra regions in response to post Little Ice Age warming, moose have inhabited river corridors several hundred kilometres north of the closed, boreal forest since they first colonized North America across the Bering Land Bridge ca. 14 000 years ago. The combination of high mobility, fluctuation-prone metapopulations, and reliance on early successional vegetation makes changes in the northern range limits of moose undependable bellwethers for other biotic responses to changing climate. The history of moose at high latitudes illustrates how understanding what happened in prehistory is useful for correctly assigning significance and cause to present-day ecological changes.

Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge.

The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n=103) and lions (Panthera spp.; n=39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.

Revisiting Distant Relations

In 2000, I published Distant Relations: How My Ancestors Colonized North America, a non-fiction exploration of my own family’s involvement in North American colonialism from the 1600s to the present. This personal essay reflects on the context, genesis, process, and consequences of writing this book during a decade of intense ferment in Indigenous–settler relations in Canada amid the revelations of horrific abuse at residential schools and the discovery that my highly respected grandfather had been involved with one. Considering the book from the perspective of 2021, I consider the strengths and limitations of this kind of critical family history and the degree to which public discourses and academic discussion of Canada’s history and settler complicity in colonialism have changed since the book was published. Arguing that critical reflection on family history is still an essential part of unlearning colonial attitudes and recognizing the systemic and structural ways that colonial disparities and processes are embedded in settler societies, I share a critical family history assignment that has been an essential and transformative pedagogical element in my university teaching for both Indigenous and non-Indigenous students.

The genomics of rapid climatic adaptation and parallel evolution in North American house mice.

Parallel changes in genotype and phenotype in response to similar selection pressures in different populations provide compelling evidence of adaptation. House mice (Mus musculus domesticus) have recently colonized North America and are found in a wide range of environments. Here we measure phenotypic and genotypic differentiation among house mice from five populations sampled across 21° of latitude in western North America, and we compare our results to a parallel latitudinal cline in eastern North America. First, we show that mice are genetically differentiated between transects, indicating that they have independently colonized similar environments in eastern and western North America. Next, we find genetically-based differences in body weight and nest building behavior between mice from the ends of the western transect which mirror differences seen in the eastern transect, demonstrating parallel phenotypic change. We then conduct genome-wide scans for selection and a genome-wide association study to identify targets of selection and candidate genes for body weight. We find some genomic signatures that are unique to each transect, indicating population-specific responses to selection. However, there is significant overlap between genes under selection in eastern and western house mouse transects, providing evidence of parallel genetic evolution in response to similar selection pressures across North America.

Million-year-old DNA sheds light on the genomic history of mammoths.

Temporal genomic data hold great potential for studying evolutionary processes, including speciation. However, sampling across speciation events would in many cases require genomic time series that stretch well into the Early Pleistocene (>1 million years). Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far is from a 560-780 ka old horse specimen2. Here we report the recovery of genome-wide data from three Early and Middle Pleistocene mammoth specimens, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these gave rise to the woolly mammoth, whereas the other represents a previously unrecognised lineage that was ancestral to the first mammoths to colonise North America. Our analyses reveal that the North American Columbian mammoth traces its ancestry to a Middle Pleistocene hybridisation between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were present already a million years ago. These findings highlight the potential of deep time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.

Dire wolves were the last of an ancient New World canid lineage.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

They Called Her Angela

Despite the arrival of African captives in other European settler communities at least 100 years before pirated Africans arrived in Virginia in 1619, it was in that colony that much of the roadmap for North America’s Black slave society was created. Virginia, after all, imported the largest numbers of Africans to North America, held resident the continent’s largest enslaved Black population in the colonial and antebellum eras, and had the first exportable cash crop, signaling that North American White wealth could be generated from Black bodies in the fields of seized Indigenous lands. One of the original captives was an Ndongo woman whom the Portuguese had named Angela. This essay attempts to move this woman from the referential margins to a more central locus as we consider the significance of 1619 in the founding of the nation’s history, the history of the Atlantic World, and the Black female diaspora. What, then, is Angela’s story? And how does it help to frame the broader context of Black women’s lives in British colonized North America?

Shared Indigenous and Crown Sovereignty: Modifying the State Model

When European nations colonized North America, their dealings with one another were based on the state model of territorial sovereignty. At the same time, they acknowledged the independence of the Indigenous nations and entered into nation-to-nation treaties with them, whereby sovereignty was to be shared. Consequently, the Westphalian concept of absolute state sovereignty has never applied in North America. While the European nations acquired sovereignty vis-a-vis one another in the international law system that they created, the Indigenous nations retained internal sovereignty and the right to continue governing themselves. This modified concept of state sovereignty has been acknowledged by the United States Supreme Court since the 1820s and is gradually being accepted in Canada. It is consistent with, and even required by, the United Nations Declaration on the Rights of Indigenous Peoples, in particular that document’s affirmation of the right of Indigenous peoples to self-determination and their right to internal self-government.

Mindful of their Bellies and gullets: Anatomical imagery in English Colonization

This essay examines the anatomical language that appears in 16th- and 17th-century English travel narratives, which authors used to portray efforts to colonize North America as a series of encounters between an American continental body and the English nation. Imagery related to the digestive tract marked struggling or failed efforts, while reproductive and marital imagery described successful ventures or encouraged new ones. The imprecision of early modern anatomical terms left them versatile enough to appear in relation to both digestive and reproductive images, allowing English observers contrasting colonial projects to provide lessons about proper modes of colonization. Anatomical language thus provided English authors with a mechanism for representing the changing nature of England’s encounter with the American continental body, redirecting anxieties about the dangers America posed into confidence about the continent’s productive potential, and England’s future on its lands.

Species delimitation and biogeography of the gnatcatchers and gnatwrens (Aves: Polioptilidae)

The New World avian family Polioptilidae (gnatcatchers and gnatwrens) is distributed from Argentina to Canada and includes 15 species and more than 60 subspecies. No study to date has evaluated phylogenetic relationships within this family and the historical pattern of diversification within the group remains unknown. Moreover, species limits, particularly in widespread taxa that show geographic variation, remain unclear. In this study, we delimited species and estimated phylogenetic relationships using multilocus data for the entire family. We then used the inferred diversity along with alternative taxonomic classification schemes to evaluate how lumping and splitting of both taxa and geographical areas influenced biogeographic inference. Species-tree analyses grouped Polioptilidae into four main clades: Microbates, Ramphocaenus, a Polioptila guianensis complex, and the remaining members of Polioptila. Ramphocaenus melanurus was sister to the clade containing M. cinereiventris and M. collaris, which formed a clade sister to all species within Polioptila. Polioptila was composed of two clades, the first of which included the P. guianensis complex; the other contained all remaining species in the genus. Using multispecies coalescent modeling, we inferred a more than 3-fold increase in species diversity, of which 87% represent currently recognized species or subspecies. Much of this diversity corresponded to subspecies that occur in the Neotropics. We identified three polyphyletic species, and delimited 4–6 previously undescribed candidate taxa. Probabilistic modeling of geographic ranges on the species tree indicated that the family likely had an ancestral origin in South America, with all three genera independently colonizing North America. Support for this hypothesis, however, was sensitive to the taxonomic classification scheme used and the number of geographical areas allowed. Our study proposes the first phylogenetic hypothesis for Polioptilidae and provides genealogical support for the reclassification of species limits. Species limits and the resolution of geographical areas that taxa inhabit influence the inferred spatial diversification history.

Large‐scale migrations of brown bears in Eurasia and to North America during the Late Pleistocene

AbstractAimClimatic changes during the Late Pleistocene had major impacts on populations of plant and animal species. Brown bears and other large mammals are likely to have experienced analogous ecological pressures and phylogeographical processes. Here, we address several unresolved issues regarding the Late Pleistocene demography of brown bears: (1) the putative locations of refugia; (2) the direction of migrations across Eurasia and into North America; and (3) parallels with the demographic histories of other wild mammals and modern humans.LocationEurasia and North America.MethodsWe sequenced 110 complete mitochondrial genomes from Eurasian brown bears and combined these with published sequences from 138 brown bears and 33 polar bears. We used a Bayesian approach to obtain a joint estimate of the phylogeny and evolutionary divergence times. The inferred mutation rate was compared with estimates obtained using two additional methods.ResultsBayesian phylogenetic analysis identified seven clades of brown bears, with most individuals belonging to a very large Holarctic clade. Bears from the widespread clade 3a1, which has a distribution from Europe across Asia to Alaska, shared a common ancestor about 45,000 years ago.Main conclusionsWe suggest that the Altai‐Sayan region and Beringia were important Late Pleistocene refuge areas for brown bears and propose large‐scale migration scenarios for bears in Eurasia and to North America. We also argue that brown bears and modern humans experienced a demographic standstill in Beringia before colonizing North America.

Fossil and genomic evidence constrains the timing of bison arrival in North America

The arrival of bison in North America marks one of the most successful large-mammal dispersals from Asia within the last million years, yet the timing and nature of this event remain poorly determined. Here, we used a combined paleontological and paleogenomic approach to provide a robust timeline for the entry and subsequent evolution of bison within North America. We characterized two fossil-rich localities in Canada's Yukon and identified the oldest well-constrained bison fossil in North America, a 130,000-y-old steppe bison, Bison cf. priscus We extracted and sequenced mitochondrial genomes from both this bison and from the remains of a recently discovered, ∼120,000-y-old giant long-horned bison, Bison latifrons, from Snowmass, Colorado. We analyzed these and 44 other bison mitogenomes with ages that span the Late Pleistocene, and identified two waves of bison dispersal into North America from Asia, the earliest of which occurred ∼195-135 thousand y ago and preceded the morphological diversification of North American bison, and the second of which occurred during the Late Pleistocene, ∼45-21 thousand y ago. This chronological arc establishes that bison first entered North America during the sea level lowstand accompanying marine isotope stage 6, rejecting earlier records of bison in North America. After their invasion, bison rapidly colonized North America during the last interglaciation, spreading from Alaska through continental North America; they have been continuously resident since then.

The asymmetry in the Great American Biotic Interchange in mammals is consistent with differential susceptibility to mammalian predation

AbstractAimOne of the most widely cited natural experiments in biogeography is the Great American Biotic Interchange (GABI). Here, we re‐assess the famous asymmetry in the exchange for mammals, with North American clades being much more successful in South America than vice versa. We investigate if this directionality could reflect higher susceptibility to predation in South American mammals rather than low competitive ability, as is usually believed.LocationNorth and South America.MethodsPrior to the GABI, South America lacked effective mammalian predators. Since its fauna did not co‐evolve with such predators, colonization of North America may only have been possible for species whose natural history makes them less susceptible to mammalian predation. To investigate this we used phylogenetic regressions to investigate species traits associated with the ability of clades originally from South America to colonize North America, and vice versa, during the GABI. Analyses were conducted both with and without species that went extinct in the late Quaternary.ResultsWhen extinct species were included, traits associated with lower predation risk (large body size, arboreality) were associated with greater success in colonizing North America for South American clades. This pattern was not visible in analyses based on the current fauna, since most of the mammals that invaded North America went extinct at the end of the Pleistocene, probably due to human predation. The pattern for northern colonizers of South America was similar whether or not extinct species were included and was not linked to predation risk.ConclusionsOur findings are consistent with the asymmetric GABI in mammals being explained by predation and not with expectations from competition. The GABI therefore illustrates that trophic interactions can be a powerful driver of long‐term dynamics of biotic interchange, as seen in many human‐driven invasions of formerly isolated regions.

Weak Polygenic Selection Drives the Rapid Adaptation of the Chemosensory System: Lessons from the Upstream Regions of the Major Gene Families.

The animal chemosensory system is involved in essential biological processes, most of them mediated by proteins encoded in multigene families. These multigene families have been fundamental for the adaptation to new environments, significantly contributing to phenotypic variation. This adaptive potential contrasts, however, with the lack of studies at their upstream regions, especially taking into account the evidence linking their transcriptional changes to certain phenotypic effects. Here, we explicitly characterize the contribution of the upstream sequences of the major chemosensory gene families to rapid adaptive processes. For that, we analyze the genome sequences of 158 lines from a population of Drosophila melanogaster that recently colonized North America, and integrate functional and transcriptional data available for this species. We find that both, strong negative and strong positive selection, shape transcriptional evolution at the genome-wide level. The chemosensory upstream regions, however, exhibit a distinctive adaptive landscape, including multiple mutations of small beneficial effect and a reduced number of cis-regulatory elements. Together, our results suggest that the promiscuous and partially redundant transcription and function of the chemosensory genes provide evolutionarily opportunities for rapid adaptive episodes through weak polygenic selection.

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

SummaryArabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.