Phylogeography of Arctic plants: where are we after 35 years, and where to go?

F.S. Chapin III, R.L. Jefferies, J.F. Reynolds, G.R. Shaver, and J. Svoboda, Arctic Plant Physiological Ecology: A Challenge for the Future. The Arctic System: B. Maxwell, Arctic Climate: Potential for Change under Global Warming. D.L. Kane, L.D. Hinzman, M. Woo, and K.R. Everett, Arctic Hydrology and Climate Change. L.C. Bliss and N.V. Matveyeva, Circumpolar Arctic Vegetation. W.D. Billings, Phytogeographic and Evolutionary Potential for the Arctic Flora and Vegetation in a Changing Climate. L.C. Bliss and K.M. Peterson, Plant Succession, Competition, and the Physiological Constraints of Species in the Arctic. Carbon Balance: W.C. Oechel and W.D. Billings, Effects of Global Change on the Carbon Balance of Arctic Plants and Ecosystems. O.A. Semikhatova, T.V. Gerasimenko, and T.I. Ivanova, Photosynthesis, Respiration, and Growth of Plants in the Soviet Arctic. G.R. Shaver and J. Kummerow, Phenology, Resource Allocation, and Growth of Arctic Vascular Plants. J.D. Tenhunen, O.L. Lange, S. Hahn, R. Siegwolf, and S.F. Oberbauer, The Ecosystem Role of Poikilohydric Tundra Plants. B. Sveinbj~adornsson, Arctic Tree Line in a Changing Climate. Water and Nutrient Balance: S.F. Oberbauer and T.E. Dawson, Water Relations of Arctic Vascular Plants. K.J. Nadelhoffer, A.E. Giblin, G.R. Shaver, and A.E. Linkins, Microbial Processes and Plant Nutrient Availability in Arctic Soils. D.M. Chapin and C.S. Bledsoe, Nitrogen Fixation in Arctic Plant Communities. K. Kielland and F.S. Chapin III, Nutrient Absorption and Accumulation in Arctic Plants. F. Berendse and S. Jonasson, Nutrient Use and Nutrient Cycling in Northern Ecosystems. Interactions: J.B. McGraw and N. Fetcher, Response of Tundra Plant Populations to Climatic Change. J.P. Bryant and P.B. Reichardt, Controls over Secondary Metabolite Production by Arctic Woody Plants. R.L. Jefferies, J. Svoboda, G. Henry, M. Raillard, and R. Ruess, Tundra Grazing Systems and Climatic Change. J.F. Reynolds and P.W. Leadley, Modeling the Response of Arctic Plants to Changing Climate. F.S. Chapin III, R.L. Jefferies, J.F. Reynolds, G.R. Shaver, and J. Svoboda, Arctic Plant Physiological Ecology in an Ecosystem Context. Index.

Opportunities for unlocking the potential of genomics for African trees.

Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs.

Phenology is the timing of nature’s seasonal events. Ambient temperature plays a key role in phenology and hence, as the climate warms, phenology will likely change. This thesis studied the impact of Arctic climate change on Arctic plant flowering and fruiting phenology in Nunavut, Canada. To establish a baseline for current plant phenology, the first question asked was ‘How does flowering phenology vary across Nunavut?’. Contrary to what might be expected, plants at a more northerly location flower earlier or at the same time and for a shorter duration than conspecifics at a more southerly location. Observations of vast differences in flower abundance in three consecutive and climatically-contrasting years highlighted the challenges of reproductive success with weather extremes associated with contemporary climate change given that Arctic plants require three plus years to complete the sexual reproductive cycle. Finally, three methods, employing long-term phenology monitoring, historical phenological records and an elevation gradient, combined with temperature records, were used to ask the questions: ‘How have temperatures in Nunavut changed?’, ‘How have Nunavut Arctic flowering and fruiting times responded to climate change?’ and ‘What is the predicted temperature-sensitivity of Arctic plants to rising temperatures of climate change?’. Annual temperatures in Nunavut are rising faster than the global average. However, in contrast to temperate regions where spring temperatures are rising the most, monthly temperatures in late summer, autumn and winter are rising significantly in Nunavut. Later-flowering species have advanced flowering times more than early-flowering species and seed dispersal times have advanced more than flowering times. Flowering time temperature-sensitivity is species specific and Nunavut region specific with mid-summer-flowering species more sensitive than early- and late-flowering species and Nunavut Arctic archipelago plants more sensitive than Nunavut mainland conspecifics. That Arctic plants’ reproductive phenological events are temperature-sensitive is a good news story suggesting that they will respond to climate change and possibly experience greater reproductive success. Interspecific and inter-regional variation in phenological temperature-sensitivity suggests Arctic plant ecological community structure will alter with climate change but differentially across Nunavut.

Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk

Ancient DNA has emerged as a powerful tool for investigating the human past and reconstructing the movements, mixtures, and adaptations that have structured genetic variation throughout human history. While the study of genome-wide ancient human DNA was initially restricted to regions with temperate climates, methodological breakthroughs have now extended the reach of ancient DNA analysis to parts of the world with hot and humid climates that are less conducive to biomolecular preservation. This includes Africa, where people harbor more genetic diversity than can be found anywhere else on the planet, reflecting deep and complex population histories. Since the first ancient African genome was published in 2015, the number of individuals with genome-wide data has increased to nearly 200, with greater coverage of diverse geographical, temporal, and cultural contexts. Ancient DNA sequences have revealed genetic variation in ancient African foragers that no longer exists in unadmixed form; illuminated how local-, regional-, and continental-scale demographic processes associated with the spread of food production and new technologies changed genetic landscapes; and discerned notable variation in interactions among people with distinct genetic ancestries, cultural practices, and, likely, languages. Despite an increasing number of studies focused on African ancient DNA, multiple regions and time periods have yet to be explored. Research to date has primarily focused on the past several thousand years in eastern and southern Africa, setting up northern, western, and central Africa, as well as deeper time periods, as key areas for future investigation. As ancient DNA research becomes increasingly integrated with anthropology and archaeology, it is advantageous to understand the basic methodological and analytical techniques, the types of questions that can be investigated, and the ways in which the discipline may continue to grow and evolve. Critically, the growth and evolution of ancient DNA research must include attention to the ethics of this work, both in African contexts and globally. In particular, it is essential that research is conducted in a way that minimizes the potential of harm to both the living and the dead. Scientists conducting ancient DNA research in Africa especially must also contend with structural challenges, including a lack of ancient DNA facilities on the continent, the extensive fragmentation of African heritage (including ancient human remains) among curating institutions worldwide, and the complexities of identifying descendant groups and other stakeholders in the wake of colonial and postcolonial disruptions and displacements. Ancient DNA research projects should be designed in a way that contributes to capacity building and the reduction of inequities between the Global North and South to ensure that the research benefits the people and communities with connections to the ancient individuals studied. While ensuring that future studies are rooted in ethical and equitable practices will require considerable collective action, ancient DNA research has already become an integral part of our understanding of African population history and will continue to shape our understanding of the African past.

Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.

Whole genome sequencing for generating SNP data is increasingly used in population genetic studies. However, obtaining genomes for massive numbers of samples is still not within the budgets of many researchers. It is thus imperative to select an appropriate reference genome and sequencing depth to ensure the accuracy of the results for a specific research question, while balancing cost and feasibility. To evaluate the effect of the choice of the reference genome and sequencing depth on downstream analyses, we used five confamilial reference genomes of variable relatedness and three levels of sequencing depth (3.5×, 7.5× and 12×) in a population genomic study on two caddisfly species: Himalopsyche digitata and H. tibetana. Using these 30 datasets (five reference genomes × three depths × two target species), we estimated population genetic indices (inbreeding coefficient, nucleotide diversity, pairwise FST, and genome‐wide distribution of FST) based on variants and population structure (PCA and admixture) based on genotype likelihood estimates. The results showed that both distantly related reference genomes and lower sequencing depth lead to degradation of resolution. In addition, choosing a more closely related reference genome may significantly remedy the defects caused by low depth. Therefore, we conclude that population genetic studies would benefit from closely related reference genomes, especially as the costs of obtaining a high‐quality reference genome continue to decrease. However, to determine a cost‐efficient strategy for a specific population genomic study, a trade‐off between reference genome relatedness and sequencing depth can be considered.

Studies of modern and ancient DNA (aDNA) have substantially improved our understanding of the early history of human populations. Despite advances in whole-genome sequencing technologies, present studies of aDNA are largely based on a panel of preselected genomic variants; thus, valuable genetic information in aDNA should be further explored. This study analyzed genotype data from 19 ancient and 16 modern high-coverage shotgun human genomes. We used modern populations from the 1000 Genomes Project and the Human Genome Diversity Project as reference populations and selected single-nucleotide polymorphisms (SNPs) that were polymorphic in one reference population and monomorphic in the others. Ancestral spectrum analyses based on the population-specific SNPs were conducted on the 19 aDNA and 16 modern DNA samples to determine their coancestries with modern reference populations. These analyses effectively revealed the genetic affinity between aDNA and modern populations, which is also true for modern DNA. The results for the 11 aDNA samples with expected transition-to-transversion ratios agree with previous analyses; the 8 aDNA samples with excessive transition-to-transversion ratios revealed ancestral spectra indicative of a high level of DNA damage that cannot be fully explained by postmortem cytosine deamination. Additional biochemistry or bioinformatics treatments seem necessary for the meaningful study of such aDNA.

abstract: Studies of modern and ancient DNA (aDNA) have substantially improved our understanding of the early history of human populations. Despite advances in whole-genome sequencing technologies, present studies of aDNA are largely based on a panel of preselected genomic variants; thus, valuable genetic information in aDNA should be further explored. This study analyzed genotype data from 19 ancient and 16 modern high-coverage shotgun human genomes. We used modern populations from the 1000 Genomes Project and the Human Genome Diversity Project as reference populations and selected single-nucleotide polymorphisms (SNPs) that were polymorphic in one reference population and monomorphic in the others. Ancestral spectrum analyses based on the population-specific SNPs were conducted on the 19 aDNA and 16 modern DNA samples to determine their coancestries with modern reference populations. These analyses effectively revealed the genetic affinity between aDNA and modern populations, which is also true for modern DNA. The results for the 11 aDNA samples with expected transition-to-transversion ratios agree with previous analyses; the 8 aDNA samples with excessive transition-to-transversion ratios revealed ancestral spectra indicative of a high level of DNA damage that cannot be fully explained by postmortem cytosine deamination. Additional biochemistry or bioinformatics treatments seem necessary for the meaningful study of such aDNA.

The Torreya Guardians are trying to save the Florida torreya (Torreya taxifolia Arn.) from extinction (Barlow & Martin 2004). Fewer than 1000 individuals of this coniferous tree remain within its native distribution, a 35-km stretch of the Apalachicola River, and these trees are not reproducing (Schwartz et al. 2000). Even if the Florida torreya was not declining toward extinction, the species would be at risk from climate change. Warming is projected to either significantly reduce or eliminate suitable habitat for most narrowly endemic taxa (Thomas et al. 2004; Hannah et al. 2005; Peterson et al. 2006), forcing species to colonize new terrain to survive. The focus of the Torreya Guardians is an “assisted migration” program that would introduce seedlings to forests across the Southern Appalachians and Cumberland Plateau (http://www.TorreyaGuardians.org). Their intent is to avert extinction by deliberately expanding the range of this endangered plant over 500 km northward. Because planting endangered plants in new environments is relatively simple as long as seeds are legally acquired and planted with landowner permission, the Torreya Guardians believe their efforts are justified. Introducing this species to regions where it has not existed for 65 million years is “[e]asy, legal, and cheap” (Barlow & Martin 2004). If circumventing climate-driven extinction is a conservation priority, then assisted migration must be considered a management option. Compelling evidence suggests that climate change will be a significant driver of extinction (McCarthy et al. 2001; McLaughlin et al. 2002; Root et al. 2003; Thomas et al. 2004). Researchers typically conclude that mitigating climate change and providing reserve networks that foster connectivity and movement should be a priority (e.g., Hannah et al. 2002). Ecol-

The giant panda was widely distributed in China and south-eastern Asia during the middle to late Pleistocene, prior to its habitat becoming rapidly reduced in the Holocene. While conservation reserves have been established and population numbers of the giant panda have recently increased, the interpretation of its genetic diversity remains controversial. Previous analyses, surprisingly, have indicated relatively high levels of genetic diversity raising issues concerning the efficiency and usefulness of reintroducing individuals from captive populations. However, due to a lack of DNA data from fossil specimens, it is unknown whether genetic diversity was even higher prior to the most recent population decline. We amplified complete cytb and 12s rRNA, partial 16s rRNA and ND1, and control region sequences from the mitochondrial genomes of two Holocene panda specimens. We estimated genetic diversity and population demography by analyzing the ancient mitochondrial DNA sequences alongside those from modern giant pandas, as well as from other members of the bear family (Ursidae). Phylogenetic analyses show that one of the ancient haplotypes is sister to all sampled modern pandas and the second ancient individual is nested among the modern haplotypes, suggesting that genetic diversity may indeed have been higher earlier during the Holocene. Bayesian skyline plot analysis supports this view and indicates a slight decline in female effective population size starting around 6000 years B.P., followed by a recovery around 2000 years ago. Therefore, while the genetic diversity of the giant panda has been affected by recent habitat contraction, it still harbors substantial genetic diversity. Moreover, while its still low population numbers require continued conservation efforts, there seem to be no immediate threats from the perspective of genetic evolutionary potential.

Landscape genetics of the widespread ground-beetle Carabus auratus in an agricultural region

AimHigh intra‐specific genetic diversity is necessary for species adaptation to novel environments under climate change, but species tracking suitable conditions are losing alleles through successive founder events during range shift. Here, we investigated the relationship between range shift since the Last Glacial Maximum (LGM) and extant population genetic diversity across multiple plant species to understand variability in species responses.LocationThe circumpolar Arctic and northern temperate alpine ranges.MethodsWe estimated the climatic niches of 30 cold‐adapted plant species using range maps coupled with species distribution models and hindcasted species suitable areas to reconstructions of the mid‐Holocene and LGM climates. We computed the species‐specific migration distances from the species glacial refugia to their current distribution and correlated distances to extant genetic diversity in 1295 populations. Differential responses among species were related to life‐history traits.ResultsWe found a negative association between inferred migration distances from refugia and genetic diversities in 25 species, but only 11 had statistically significant negative slopes. The relationships between inferred distance and population genetic diversity were steeper for insect‐pollinated species than wind‐pollinated species, but the difference among pollination system was marginally independent from phylogenetic autocorrelation.Main conclusionThe relationships between inferred migration distances and genetic diversities in 11 species, independent from current isolation, indicate that past range shifts were associated with a genetic bottleneck effect with an average of 21% loss of genetic diversity per 1000 km−1. In contrast, the absence of relationship in many species also indicates that the response is species specific and may be modulated by plant pollination strategies or result from more complex historical contingencies than those modelled here.

Spread and performance of European earthworms invading North America as indicated by molecular markers and climate chamber experiments