Title: An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods
Abstract
Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group. Novel approaches to identify distinctive genetic lineages, including unsupervised machine learning variational autoencoder plots, were used to establish species hypothesis frameworks. In this sense, three undescribed species and a complex of cryptic species were identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further observed that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study agrees on how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.
Baker, Caitlin M.; Boyer, Sarah L.; Giribet, Gonzalo(
, Journal of Biogeography)
AbstractAim
We explored the extent to which Gondwanan vicariance contributed to the circum‐Antarctic distribution of the mite harvestman family Pettalidae, a group of small, dispersal‐limited arachnids whose phylogeny has been poorly resolved, precluding rigorous biogeographic hypothesis testing.
Location
Continental landmasses of former temperate Gondwana (Chile, South Africa, Sri Lanka, Australia and New Zealand).
Taxon
Pettalidae, Opiliones.
Methods
We generated transcriptomes for a phylogeny of 16 pettalids, spanning 9 genera. Data were analysed using maximum likelihood, Bayesian inference and coalescence methods. The phylogenetic position of the Sri Lankan genusPettaluswas further explored using quartet likelihood mapping and changes in gene likelihood scores. We also estimated divergence times and looked for signatures of extinction across Antarctica and central Australia using previously published phylogenies with near‐complete species sampling constrained to match our transcriptomic results. Finally, we estimated ancestral ranges and inferred instances of vicariance.
Results
We recovered a well‐supported topology with a division between taxa from landmasses that made up East Gondwana, and a grade of taxa from West Gondwana.Pettaluswas resolved either as the sister group of the Queensland‐endemicAustropurcellia, or as the sister group to a larger clade from East Gondwana, though favouringPettalus + Austropurcellia. Divergence times for multiple vicariance events coincided with Gondwana's breakup. Speciation–extinction analysis found one diversification process for the family: an initial burst of cladogenesis that slowed down through time.
Main Conclusions
Given that the order of cladogenesis corresponds to the order in which Gondwana fragmented, and the concurrent timing of vicariance and rifting, Gondwanan breakup explains major biogeographic patterns in Pettalidae. Some divergences predate initial rifting, but there is no evidence oftrans‐oceanic dispersal. The Sri Lanka–eastern Australia relationship makes sense in the light of large‐scale extinction across Antarctica and central Australia; however, we find no clear signatures of mass extinction.
IODP Expedition 379 to the Amundsen Sea continental rise recovered latest Miocene-Holocene sediments from two sites on a drift in water depths >3900m. Sediments that are dominated by clay and silty clay host pebbles and cobbles of ice-rafted detritus (IRD) (Gohl et al. 2021, doi: 10.14379/iodp.proc.379.2021). Cobble-sized dropstones also appear as fall-in, in the top of cores recovered from sediments >5.3 Ma. The principle means to deposit abundant IRD and sparse dropstones in deep sea sediment is through melting of icebergs released by Antarctic ice-sheet calving events. We use petrological and age characteristics of clasts from the Exp379 sites to fingerprint their bedrock provenance to extend knowledge of subglacial bedrock, and with the intention to illuminate changes in icesheet extent between 7 – 3 Ma that lend credence to forecasts of extensive future change.
Mapped onshore geology shows pronounced distinctions in bedrock age between tectonic provinces of West or East Antarctica (e.g. Cox et al. 2020, doi:10.21420/7SH7-6K05; Jordan et al. 2020, doi.org/10.1038/s43017-019-0013-6). This allows us to use geochronology and thermochronology of rock clasts and minerals for tracing their provenance, and hence ascertain whether IRD deposited at the 379 drillsites originated from proximal or distal Antarctic sources. We here report zircon and apatite U-Pb dates from several sand samples and dropstones taken from latest Miocene, early Pliocene, and Plio-Pleistocene-boundary sediments. Additional Hf isotope data, and apatite fission track and 40Ar/39Ar Kfeldspar ages for some of the same samples help to strengthen provenance interpretations.
The study revealed three distinct zircon age populations at ca. 100, 175, and 250 Ma. Using Kolmogorov-Smirnov (K-S) statistical tests to compare our new igneous and detrital zircon (DZ) U-Pb results with previously published data, we found strong similarities to West Antarctic bedrock, but low correspondence to prospective sources in East Antarctica, implying a role for icebergs calved from the West Antarctic Ice Sheet (WAIS). The ~100 Ma age resembles plutonic ages from Marie Byrd Land and islands in Pine Island Bay. The ~250 and 175 Ma populations match published mineral dates from shelf sediments in the eastern Amundsen Sea Embayment as well as granite ages from the Antarctic Peninsula and the Ellsworth-Whitmore Mountains (EWM). The different derivation of coarse sediment sources requires changes in iceberg origin through the latest Miocene, early Pliocene, and Plio/Pleistocene, likely the result of changes in WAIS extent.
One unique dropstone recovered from Exp379 Site U1533B is green quartz arenite, which yielded mostly 500-625 Ma detrital zircons. In visual appearance and dominant U-Pb age population, it resembles a sandstone dropstone recovered from Exp382 Site U1536 in the Scotia Sea (Hemming et al. 2020, https://gsa.confex.com/gsa/2020AM/meetingapp.cgi/Paper/357276). K-S tests yield high values (P ≥ 0.6), suggesting a common provenance for both dropstones recovered from late Miocene to Pliocene sediments, despite the 3270 km distance separating the sites. Comparisons to published data, in progress, narrow the group of potential on-land sources to exposures in the EWM or isolated ranges at far south latitudes in the Antarctic interior. If both dropstones originated from the same source area, they signify that dramatic shifts in the WAIS grounding line position do occur, along with periodic opening of a seaway connecting the Amundsen and Weddell Seas.
Wille, Jonathan D.; Alexander, Simon P.; Amory, Charles; Baiman, Rebecca; Barthélemy, Léonard; Bergstrom, Dana M.; Berne, Alexis; Binder, Hanin; Blanchet, Juliette; Bozkurt, Deniz; et al(
, Journal of Climate)
Abstract
Between 15 and 19 March 2022, East Antarctica experienced an exceptional heat wave with widespread 30°–40°C temperature anomalies across the ice sheet. In Part I, we assessed the meteorological drivers that generated an intense atmospheric river (AR) that caused these record-shattering temperature anomalies. Here, we continue our large collaborative study by analyzing the widespread and diverse impacts driven by the AR landfall. These impacts included widespread rain and surface melt that was recorded along coastal areas, but this was outweighed by widespread high snowfall accumulations resulting in a largely positive surface mass balance contribution to the East Antarctic region. An analysis of the surface energy budget indicated that widespread downward longwave radiation anomalies caused by large cloud-liquid water contents along with some scattered solar radiation produced intense surface warming. Isotope measurements of the moisture were highly elevated, likely imprinting a strong signal for past climate reconstructions. The AR event attenuated cosmic ray measurements at Concordia, something previously never observed. Last, an extratropical cyclone west of the AR landfall likely triggered the final collapse of the critically unstable Conger Ice Shelf while further reducing an already record low sea ice extent.
Significance Statement
Using our diverse collective expertise, we explored the impacts from the March 2022 heat wave and atmospheric river across East Antarctica. One key takeaway is that the Antarctic cryosphere is highly sensitive to meteorological extremes originating from the midlatitudes and subtropics. Despite the large positive temperature anomalies driven from strong downward longwave radiation, this event led to huge amounts of snowfall across the Antarctic interior desert. The isotopes in this snow of warm airmass origin will likely be detectable in future ice cores and potentially distort past climate reconstructions. Even measurements of space activity were affected. Also, the swells generated from this storm helped to trigger the final collapse of an already critically unstable Conger Ice Shelf while further degrading sea ice coverage.
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 underside 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.
Gohl, K.; Wellner, J.S.; Klaus, A.(
, 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 impinging 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.
@article{osti_10225958,
place = {Country unknown/Code not available},
title = {An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods},
url = {https://par.nsf.gov/biblio/10225958},
DOI = {10.1038/s41598-021-87244-5},
abstractNote = {Abstract Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group. Novel approaches to identify distinctive genetic lineages, including unsupervised machine learning variational autoencoder plots, were used to establish species hypothesis frameworks. In this sense, three undescribed species and a complex of cryptic species were identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further observed that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study agrees on how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.},
journal = {Scientific Reports},
volume = {11},
number = {1},
publisher = {Nature Publishing Group},
author = {Moles, Juan and Derkarabetian, Shahan and Schiaparelli, Stefano and Schrödl, Michael and Troncoso, Jesús S. and Wilson, Nerida G. and Giribet, Gonzalo},
}
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