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1. Origin and Diversification of the Saguaro Cactus ( Carnegiea gigantea ): A Within-Species Phylogenomic Analysis

   https://doi.org/10.1093/sysbio/syac017  

   Sanderson, Michael J. ; Búrquez, Alberto ; Copetti, Dario ; McMahon, Michelle M. ; Zeng, Yichao ; Wojciechowski, Martin F. ; Solis-Lemus, ed., Claudia ( March 2022 , Systematic Biology)

   Reconstructing accurate historical relationships within a species poses numerous challenges, not least in many plant groups in which gene flow is high enough to extend well beyond species boundaries. Nonetheless, the extent of tree-like history within a species is an empirical question on which it is now possible to bring large amounts of genome sequence to bear. We assess phylogenetic structure across the geographic range of the saguaro cactus, an emblematic member of Cactaceae, a clade known for extensive hybridization and porous species boundaries. Using 200 Gb of whole genome resequencing data from 20 individuals sampled from 10 localities, we assembled two data sets comprising 150,000 biallelic single nucleotide polymorphisms (SNPs) from protein coding sequences. From these, we inferred within-species trees and evaluated their significance and robustness using five qualitatively different inference methods. Despite the low sequence diversity, large census population sizes, and presence of wide-ranging pollen and seed dispersal agents, phylogenetic trees were well resolved and highly consistent across both data sets and all methods. We inferred that the most likely root, based on marginal likelihood comparisons, is to the east and south of the region of highest genetic diversity, which lies along the coast of the Gulfmore »of California in Sonora, Mexico. Together with striking decreases in marginal likelihood found to the north, this supports hypotheses that saguaro’s current range reflects postglacial expansion from the refugia in the south of its range. We conclude with observations about practical and theoretical issues raised by phylogenomic data sets within species, in which SNP-based methods must be used rather than gene tree methods that are widely used when sequence divergence is higher. These include computational scalability, inference of gene flow, and proper assessment of statistical support in the presence of linkage effects. [Phylogenomics; phylogeography; rooting; Sonoran Desert.]

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2. Amundsen Sea West Antarctic Ice Sheet History

   https://doi.org/10.14379/iodp.proc.379.2021  

   Gohl, K. ; Wellner, J.S. ; Klaus, A. ( February 2021 , Proceedings of the International Ocean Discovery Program)

   The Amundsen Sea sector of Antarctica has long been considered the most vulnerable part of the West Antarctic Ice Sheet (WAIS) because of the great water depth at the grounding line, a subglacial bed seafloor deepening toward the interior of the continent, and the absence of substantial ice shelves. Glaciers in this configuration are thought to be susceptible to rapid or runaway retreat. Ice flowing into the Amundsen Sea Embayment is undergoing the most rapid changes of any sector of the Antarctic ice sheets outside the Antarctic Peninsula, including substantial grounding-line retreat over recent decades, as observed from satellite data. Recent models suggest that a threshold leading to the collapse of WAIS in this sector may have been already crossed and that much of the ice sheet could be lost even under relatively moderate greenhouse gas emission scenarios. Drill cores from the Amundsen Sea provide tests of several key questions about controls on ice sheet stability. The cores offer a direct offshore record of glacial history in a sector that is exclusively influenced by ice draining the WAIS, which allows clear comparisons between the WAIS history and low-latitude climate records. Today, relatively warm (modified) Circumpolar Deep Water (CDW) is impingingmore »onto the Amundsen Sea shelf and causing melting under ice shelves and at the grounding line of the WAIS in most places. Reconstructions of past CDW intrusions can assess the ties between warm water upwelling and large-scale changes in past grounding-line positions. Carrying out these reconstructions offshore from the drainage basin that currently has the most substantial negative mass balance of ice anywhere in Antarctica is thus of prime interest to future predictions. The scientific objectives for this expedition are built on hypotheses about WAIS dynamics and related paleoenvironmental and paleoclimatic conditions. The main objectives are: 1. To test the hypothesis that WAIS collapses occurred during the Neogene and Quaternary and, if so, when and under which environmental conditions; 2. To obtain ice-proximal records of ice sheet dynamics in the Amundsen Sea that correlate with global records of ice-volume changes and proxy records for atmospheric and ocean temperatures; 3. To study the stability of a marine-based WAIS margin and how warm deepwater incursions control its position on the shelf; 4. To find evidence for the earliest major grounded WAIS advances onto the middle and outer shelf; 5. To test the hypothesis that the first major WAIS growth was related to the uplift of the Marie Byrd Land dome. International Ocean Discovery Program (IODP) Expedition 379 completed two very successful drill sites on the continental rise of the Amundsen Sea. Site U1532 is located on a large sediment drift, now called the Resolution Drift, and it penetrated to 794 m with 90% recovery. We collected almost-continuous cores from recent age through the Pleistocene and Pliocene and into the upper Miocene. At Site U1533, we drilled 383 m (70% recovery) into the more condensed sequence at the lower flank of the same sediment drift. The cores of both sites contain unique records that will enable study of the cyclicity of ice sheet advance and retreat processes as well as ocean-bottom water circulation and water mass changes. In particular, Site U1532 revealed a sequence of Pliocene sediments with an excellent paleomagnetic record for high-resolution climate change studies of the previously sparsely sampled Pacific sector of the West Antarctic margin. Despite the drilling success at these sites, the overall expedition experienced three unexpected difficulties that affected many of the scientific objectives: 1. The extensive sea ice on the continental shelf prevented us from drilling any of the proposed shelf sites. 2. The drill sites on the continental rise were in the path of numerous icebergs of various sizes that frequently forced us to pause drilling or leave the hole entirely as they approached the ship. The overall downtime caused by approaching icebergs was 50% of our time spent on site. 3. A medical evacuation cut the expedition short by 1 week. Recovery of core on the continental rise at Sites U1532 and U1533 cannot be used to indicate the extent of grounded ice on the shelf or, thus, of its retreat directly. However, the sediments contained in these cores offer a range of clues about past WAIS extent and retreat. At Sites U1532 and U1533, coarse-grained sediments interpreted to be ice-rafted debris (IRD) were identified throughout all recovered time periods. A dominant feature of the cores is recorded by lithofacies cyclicity, which is interpreted to represent relatively warmer periods variably characterized by sediments with higher microfossil abundance, greater bioturbation, and higher IRD concentrations alternating with colder periods characterized by dominantly gray laminated terrigenous muds. Initial comparison of these cycles to published late Quaternary records from the region suggests that the units interpreted to be records of warmer time intervals in the core tie to global interglacial periods and the units interpreted to be deposits of colder periods tie to global glacial periods. Cores from the two drill sites recovered sediments of dominantly terrigenous origin intercalated or mixed with pelagic or hemipelagic deposits. In particular, Site U1533, which is located near a deep-sea channel originating from the continental slope, contains graded silts, sands, and gravels transported downslope from the shelf to the rise. The channel is likely the pathway of these sediments transported by turbidity currents and other gravitational downslope processes. The association of lithologic facies at both sites predominantly reflects the interplay of downslope and contouritic sediment supply with occasional input of more pelagic sediment. Despite the lack of cores from the shelf, our records from the continental rise reveal the timing of glacial advances across the shelf and thus the existence of a continent-wide ice sheet in West Antarctica during longer time periods since at least the late Miocene. Cores from both sites contain abundant coarse-grained sediments and clasts of plutonic origin transported either by downslope processes or by ice rafting. If detailed provenance studies confirm our preliminary assessment that the origin of these samples is from the plutonic bedrock of Marie Byrd Land, their thermochronological record will potentially reveal timing and rates of denudation and erosion linked to crustal uplift. The chronostratigraphy of both sites enables the generation of a seismic sequence stratigraphy for the entire Amundsen Sea continental rise, spanning the area offshore from the Amundsen Sea Embayment westward along the Marie Byrd Land margin to the easternmost Ross Sea through a connecting network of seismic lines.« less
3. Expedition 379 Preliminary Report: Amundsen Sea West Antarctic Ice Sheet History

   https://doi.org/10.14379/iodp.pr.379.2019  

   Gohl, K. ; Wellner, J.S. ; Klaus, A. ( May 2019 , Preliminary report)

   The Amundsen Sea sector of Antarctica has long been considered the most vulnerable part of the West Antarctic Ice Sheet (WAIS) because of the great water depth at the grounding line and the absence of substantial ice shelves. Glaciers in this configuration are thought to be susceptible to rapid or runaway retreat. Ice flowing into the Amundsen Sea Embayment is undergoing the most rapid changes of any sector of the Antarctic Ice Sheet outside the Antarctic Peninsula, including changes caused by substantial grounding-line retreat over recent decades, as observed from satellite data. Recent models suggest that a threshold leading to the collapse of WAIS in this sector may have been already crossed and that much of the ice sheet could be lost even under relatively moderate greenhouse gas emission scenarios. Drill cores from the Amundsen Sea provide tests of several key questions about controls on ice sheet stability. The cores offer a direct record of glacial history offshore from a drainage basin that receives ice exclusively from the WAIS, which allows clear comparisons between the WAIS history and low-latitude climate records. Today, warm Circumpolar Deep Water (CDW) is impinging onto the Amundsen Sea shelf and causing melting of the undersidemore »of the WAIS in most places. Reconstructions of past CDW intrusions can assess the ties between warm water upwelling and large-scale changes in past grounding-line positions. Carrying out these reconstructions offshore from the drainage basin that currently has the most substantial negative mass balance of ice anywhere in Antarctica is thus of prime interest to future predictions. The scientific objectives for this expedition are built on hypotheses about WAIS dynamics and related paleoenvironmental and paleoclimatic conditions. The main objectives are 1. To test the hypothesis that WAIS collapses occurred during the Neogene and Quaternary and, if so, when and under which environmental conditions; 2. To obtain ice-proximal records of ice sheet dynamics in the Amundsen Sea that correlate with global records of ice-volume changes and proxy records for atmospheric and ocean temperatures; 3. To study the stability of a marine-based WAIS margin and how warm deep-water incursions control its position on the shelf; 4. To find evidence for earliest major grounded WAIS advances onto the middle and outer shelf; 5. To test the hypothesis that the first major WAIS growth was related to the uplift of the Marie Byrd Land dome. International Ocean Discovery Program (IODP) Expedition 379 completed two very successful drill sites on the continental rise of the Amundsen Sea. Site U1532 is located on a large sediment drift, now called Resolution Drift, and penetrated to 794 m with 90% recovery. We collected almost-continuous cores from the Pleistocene through the Pliocene and into the late Miocene. At Site U1533, we drilled 383 m (70% recovery) into the more condensed sequence at the lower flank of the same sediment drift. The cores of both sites contain unique records that will enable study of the cyclicity of ice sheet advance and retreat processes as well as bottom-water circulation and water mass changes. In particular, Site U1532 revealed a sequence of Pliocene sediments with an excellent paleomagnetic record for high-resolution climate change studies of the previously sparsely sampled Pacific sector of the West Antarctic margin. Despite the drilling success at these sites, the overall expedition experienced three unexpected difficulties that affected many of the scientific objectives: 1. The extensive sea ice on the continental shelf prevented us from drilling any of the proposed shelf sites. 2. The drill sites on the continental rise were in the path of numerous icebergs of various sizes that frequently forced us to pause drilling or leave the hole entirely as they approached the ship. The overall downtime caused by approaching icebergs was 50% of our time spent on site. 3. An unfortunate injury to a member of the ship's crew cut the expedition short by one week. Recovery of core on the continental rise at Sites U1532 and U1533 cannot be used to precisely indicate the position of ice or retreat of the ice sheet on the shelf. However, these sediments contained in the cores offer a range of clues about past WAIS extent and retreat. At Sites U1532 and U1533, coarse-grained sediments interpreted to be ice-rafted debris (IRD) were identified throughout all recovered time periods. A dominant feature of the cores is recorded by lithofacies cyclicity, which is interpreted to represent relatively warmer periods variably characterized by higher microfossil abundance, greater bioturbation, and higher counts of IRD alternating with colder periods characterized by dominantly gray laminated terrigenous muds. Initial comparison of these cycles to published records from the region suggests that the units interpreted as records of warmer time intervals in the core tie to interglacial periods and the units interpreted as deposits of colder periods tie to glacial periods. The cores from the two drill sites recovered sediments of purely terrigenous origin intercalated or mixed with pelagic or hemipelagic deposits. In particular, Site U1533, which is located near a deep-sea channel originating from the continental slope, contains graded sands and gravel transported downslope from the shelf to the abyssal plain. The channel is likely the path of such sediments transported downslope by turbidity currents or other sediment-gravity flows. The association of lithologic facies at both sites predominantly reflects the interplay of downslope and contouritic sediment supply with occasional input of more pelagic sediment. Despite the lack of cores from the shelf, our records from the continental rise reveal the timing of glacial advances across the shelf and thus the existence of a continent-wide ice sheet in West Antarctica at least during longer time periods since the late Miocene. Cores from both sites contain abundant coarse-grained sediments and clasts of plutonic origin transported either by downslope processes or by ice rafting. If detailed provenance studies confirm our preliminary assessment that the origin of these samples is from the plutonic bedrock of Marie Byrd Land, their thermochronological record will potentially reveal timing and rates of denudation and erosion linked to crustal uplift. The chronostratigraphy of both sites enables the generation of a seismic sequence stratigraphy not only for the Amundsen Sea rise but also for the western Amundsen Sea along the Marie Byrd Land margin through a connecting network of seismic lines.« less
4. Vegetation stability and the habitat associations of the endemic taxa of the Olympic Peninsula, Washington, USA

   Gavin, Daniel G. ( April 2015 , Frontiers of biogeography)

   Explanations for areas of endemism often involve relative climatic stability, or low climate velocity, over time scales ranging from the Pleistocene to the late Cenozoic. Given that many narrowly endemic taxa in forested landscapes display discrete habitat associations, habitat stability should be similarly important for endemic persistence. Furthermore, while past climate variability is exceedingly difficult to quantify on millennial time scales, past distributions of habitats may be robustly inferred from paleoecological records. The Olympic Peninsula, Washington, supports a biota with several insular features including 29 endemic plant and animal taxa. Here I present the geographic distribution and habitat of the endemic taxa, and then examine the vegetation stability of the past 14,300 years from five pollen records associated with discrete vegetation zones on the peninsula. I show that 11 endemics have distributions centered on dry alpine scree and rock in the northeastern quadrant of the peninsula, and nine occur in shaded riparian forests in the southwest. Vegetation turnover during the post-glacial period was smallest in these areas. However, another long pollen record from the western peninsula reveals existence of shrub tundra and greatly reduced forest cover, indicating southward displacement of shaded riparian habitats by perhaps as much as 100 km.more »Although this study supports an association of postglacial vegetation stability with endemism, records spanning the glacial maximum indicate widespread tundra during long periods of the late Pleistocene and therefore suggest southern displacement of forest-associated endemics. While some of the alpine scree-associated endemics may have persisted in situ, many others likely arrived via a variety of dispersal trajectories. These histories include dispersal from southern refugia towards ocean barriers preventing further northward dispersal, contraction from more widespread distributions, and recent divergence from sister taxa. This study shows that paleoecological records can cast strong doubt on the inference that areas of endemism necessarily imply in situ glacial survival.« less
5. Ancient boreal forests under the environmental instability of the glacial to postglacial transition in the Great Lakes region (14 000 – 11 000 years BP)

   https://doi.org/10.1139/cjfr-2012-0339  

   Panyushkina, Irina P. ; Leavitt, Steven W. ( November 2013 , Canadian Journal of Forest Research)

   Retreat of the Laurentide Ice Sheet 20 000 years ago tremendously altered environmental conditions and opened territory to the boreal spruce forest expansion. However, the details of forest colonization during the rapid climate warming and the adaptation of the newly developed stands to short cooling episodes during the warming and degradation of the ice sheet are not known. Preservation of wood from the glacial to postglacial transition offers the opportunity for examination of high-frequency growth variability in response to hemispheric and local forcings on temperature and hydrology. Here we consider growth of spruce at three sites from the interior of Northern America developed at ca. 13 700, 12 100, and 11 300 calibrated years before present (cal years BP), with well-replicated tree-ring chronologies spanning from 116 to 310 years. The data show at least two generations of trees established at each of the sites promoted by short, warm intervals. The tree mortality was variously affected by both cold conditions and the influence of rising water table and sediment burial. The history of these stands indicates breaks in forest colonization following a century (or two) of successful migrations. Interestingly, the thinning of the spruce forest did not seem to open pioneering opportunities for other treemore »species at those times.« less