INTRODUCTION Resolving the role that different environmental forces may have played in the apparent explosive diversification of modern placental mammals is crucial to understanding the evolutionary context of their living and extinct morphological and genomic diversity. RATIONALE Limited access to whole-genome sequence alignments that sample living mammalian biodiversity has hampered phylogenomic inference, which until now has been limited to relatively small, highly constrained sequence matrices often representing <2% of a typical mammalian genome. To eliminate this sampling bias, we used an alignment of 241 whole genomes to comprehensively identify and rigorously analyze noncoding, neutrally evolving sequence variation in coalescent and concatenation-based phylogenetic frameworks. These analyses were followed by validation with multiple classes of phylogenetically informative structural variation. This approach enabled the generation of a robust time tree for placental mammals that evaluated age variation across hundreds of genomic loci that are not restricted by protein coding annotations. RESULTS Coalescent and concatenation phylogenies inferred from multiple treatments of the data were highly congruent, including support for higher-level taxonomic groupings that unite primates+colugos with treeshrews (Euarchonta), bats+cetartiodactyls+perissodactyls+carnivorans+pangolins (Scrotifera), all scrotiferans excluding bats (Fereuungulata), and carnivorans+pangolins with perissodactyls (Zooamata). However, because these approaches infer a single best tree, they mask signatures of phylogenetic conflict that result from incomplete lineage sorting and historical hybridization. Accordingly, we also inferred phylogenies from thousands of noncoding loci distributed across chromosomes with historically contrasting recombination rates. Throughout the radiation of modern orders (such as rodents, primates, bats, and carnivores), we observed notable differences between locus trees inferred from the autosomes and the X chromosome, a pattern typical of speciation with gene flow. We show that in many cases, previously controversial phylogenetic relationships can be reconciled by examining the distribution of conflicting phylogenetic signals along chromosomes with variable historical recombination rates. Lineage divergence time estimates were notably uniform across genomic loci and robust to extensive sensitivity analyses in which the underlying data, fossil constraints, and clock models were varied. The earliest branching events in the placental phylogeny coincide with the breakup of continental landmasses and rising sea levels in the Late Cretaceous. This signature of allopatric speciation is congruent with the low genomic conflict inferred for most superordinal relationships. By contrast, we observed a second pulse of diversification immediately after the Cretaceous-Paleogene (K-Pg) extinction event superimposed on an episode of rapid land emergence. Greater geographic continuity coupled with tumultuous climatic changes and increased ecological landscape at this time provided enhanced opportunities for mammalian diversification, as depicted in the fossil record. These observations dovetail with increased phylogenetic conflict observed within clades that diversified in the Cenozoic. CONCLUSION Our genome-wide analysis of multiple classes of sequence variation provides the most comprehensive assessment of placental mammal phylogeny, resolves controversial relationships, and clarifies the timing of mammalian diversification. We propose that the combination of Cretaceous continental fragmentation and lineage isolation, followed by the direct and indirect effects of the K-Pg extinction at a time of rapid land emergence, synergistically contributed to the accelerated diversification rate of placental mammals during the early Cenozoic. The timing of placental mammal evolution. Superordinal mammalian diversification took place in the Cretaceous during periods of continental fragmentation and sea level rise with little phylogenomic discordance (pie charts: left, autosomes; right, X chromosome), which is consistent with allopatric speciation. By contrast, the Paleogene hosted intraordinal diversification in the aftermath of the K-Pg mass extinction event, when clades exhibited higher phylogenomic discordance consistent with speciation with gene flow and incomplete lineage sorting.
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Earth history and the passerine superradiation
Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
more » « less- NSF-PAR ID:
- 10089764
- Author(s) / Creator(s):
- ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; ; more »
- Publisher / Repository:
- Proceedings of the National Academy of Sciences
- Date Published:
- Journal Name:
- Proceedings of the National Academy of Sciences
- Volume:
- 116
- Issue:
- 16
- ISSN:
- 0027-8424
- Page Range / eLocation ID:
- p. 7916-7925
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract The origin of taxa presenting a disjunct distribution between Africa and Asia has puzzled biogeographers for more than a century. This biogeographic pattern has been hypothesized to be the result of transoceanic long‐distance dispersal, Oligocene dispersal through forested corridors, Miocene dispersal through the Arabian Peninsula or passive dispersal on the rifting Indian plate. However, it has often been difficult to pinpoint the mechanisms at play. We investigate biotic exchange between the Afrotropics and the Oriental region during the Cenozoic, a period in which geological changes altered landmass connectivity. We use Baorini skippers (Lepidoptera, Hesperiidae) as a model, a widespread clade of butterflies in the Old World tropics with a disjunct distribution between the Afrotropics and the Oriental region. We use anchored phylogenomics to infer a robust evolutionary tree for Baorini skippers and estimate divergence times and ancestral ranges to test biogeographic hypotheses. Our phylogenomic tree recovers strongly supported relationships for Baorini skippers and clarifies the systematics of the tribe. Dating analyses suggest that these butterflies originated in the Oriental region, Greater Sunda Islands, and the Philippines in the early Miocene
c . 23 Ma. Baorini skippers dispersed from the Oriental region towards Africa at least five times in the past 20 Ma. These butterflies colonized the Afrotropics primarily through trans‐Arabian geodispersal after the closure of the Tethyan seaway in the mid‐Miocene. Range expansion from the Oriental region towards the African continent probably occurred via theGomphotherium land bridge through the Arabian Peninsula. Alternative scenarios invoking long‐distance dispersal and vicariance are not supported. The Miocene climate change and biome shift from forested areas to grasslands possibly facilitated geodispersal in this clade of butterflies. -
null (Ed.)The tectonic and paleoceanographic setting of the Great Australian Bight (GAB) and the Mentelle Basin (MB; adjacent to Naturaliste Plateau) offered an outstanding opportunity to investigate Cretaceous and Cenozoic climate change and ocean dynamics during the last phase of breakup among remnant Gondwana continents. Sediment recovered from sites in both regions during International Ocean Discovery Program Expedition 369 will provide a new perspective on Earth’s temperature variation at sub-polar latitudes (60°–62°S) across the extremes of the mid-Cretaceous hot greenhouse climate and the cooling that followed. The primary goals of the expedition were to • Investigate the timing and causes for the rise and collapse of the Cretaceous hot greenhouse climate and how this climate mode affected the climate-ocean system and oceanic biota; • Determine the relative roles of productivity, ocean temperature, and ocean circulation at high southern latitudes during Cretaceous oceanic anoxic events (OAEs); • Identify the main source regions for deep-water and intermediate-water masses in the southeast Indian Ocean and how these changed during Gondwana breakup; • Characterize how oceanographic conditions at the MB changed during the Cenozoic opening of the Tasman Passage and restriction of the Indonesian Gateway; • Resolve questions on the volcanic and sedimentary origins of the Australo-Antarctic Gulf and Mentelle Basin and provide stratigraphic control on the age and nature of the prebreakup successions. Hole U1512A in the GAB recovered a 691 m thick sequence of black claystone ranging from the early Turonian to the early Campanian. Age control is primarily based on calcareous nannofossils, but the presence of other microfossil groups provided consistent but low-resolution control. Despite the lithologic uniformity, long- and short-term variations in natural gamma ray and magnetic susceptibility intensities show cyclic alternations that suggest an orbital control of sediment deposition that will be useful for developing an astrochronology for the sequence. Sites U1513–U1516 were drilled between 850 and 3900 m water depth in the MB and penetrated 774, 517, 517, and 542 meters below seafloor (mbsf), respectively. Under a thin layer of Pleistocene–upper Miocene sediment, Site U1513 cored a succession of Cretaceous units from the Campanian to the Valanginian. Site U1514 sampled an expanded Pleistocene–Eocene sequence and terminated in the upper Albian. The Cenomanian–Turonian interval at Site U1514 recovered deformed sedimentary rocks that probably represent a detachment zone. Site U1515 is located on the west Australian margin at 850 m water depth and was the most challenging site to core because much of the upper 350 m was either chert or poorly consolidated sand. However, the prebreakup Jurassic(?) sediments interpreted from the seismic profiles were successfully recovered. Site U1516 cored an expanded Pleistocene, Neogene, and Paleogene section and recovered a complete Cenomanian/Turonian boundary interval containing five layers with high total organic carbon content. Recovery of well-preserved calcareous microfossil assemblages from different paleodepths will enable generation of paleotemperature and biotic records that span the rise and collapse of the Cretaceous hot greenhouse (including OAEs 1d and 2), providing insight to resultant changes in deep-water and surface water circulation that can be used to test predictions from earth system models. Paleotemperature proxies and other data will reveal the timing, magnitude, and duration of peak hothouse temperatures and any cold snaps that could have allowed growth of a polar ice sheet. The sites will also record the mid-Eocene–early Oligocene opening of the Tasman Gateway and the Miocene–Pliocene restriction of the Indonesian Gateway; both passages have important effects on global oceanography and climate. Understanding the paleoceanographic changes in a regional context provides a global test on models of Cenomanian–Turonian oceanographic and climatic evolution related both to extreme Turonian warmth and the evolution of OAE 2. The Early Cretaceous volcanic rocks and underlying Jurassic(?) sediments cored in different parts of the MB provide information on the timing of different stages of the Gondwana breakup. The recovered cores provide sufficient new age constraints to underpin a reevaluation of the basin-wide seismic stratigraphy and tectonic models for the region.more » « less
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null (Ed.)The tectonic and paleoceanographic setting of the Great Australian Bight (GAB) and the Mentelle Basin (adjacent to Naturaliste Plateau) offered an opportunity to investigate Cretaceous and Cenozoic climate change and ocean dynamics during the last phase of breakup among remnant Gondwana continents. Sediment recovered from sites in both regions during International Ocean Discovery Program Expedition 369 will provide a new perspective on Earth’s temperature variation at subpolar latitudes (60°–62°S) across the extremes of the mid-Cretaceous hot greenhouse climate and the cooling that followed. Basalts and prebreakup sediments were also recovered and will provide constraints regarding the type and age of the Mentelle Basin basement and processes operating during the break up of Gondwana. The primary goals of the expedition were to 1. Investigate the timing and causes for the rise and collapse of the Cretaceous hot greenhouse climate and how this climate mode affected the climate–ocean system and oceanic biota; 2. Determine the relative roles of productivity, ocean temperature, and ocean circulation at high southern latitudes during Cretaceous oceanic anoxic events (OAEs); 3. Investigate potential source regions for deep-water and intermediate-water masses in the southeast Indian Ocean and how these changed during Gondwana breakup; 4. Characterize how oceanographic conditions at the Mentelle Basin changed during the Cenozoic opening of the Tasman Gateway and restriction of the Indonesian Gateway; and 5. Resolve questions on the volcanic and sedimentary origins of the Australo-Antarctic Gulf and Mentelle Basin and provide stratigraphic control on the age and nature of the prebreakup successions. Hole U1512A in the GAB recovered a 691 m thick sequence of black claystone ranging from the lower Turonian to the lower Campanian. Age control is primarily based on calcareous nannofossils, but the presence of other microfossil groups provided consistent low-resolution control. Despite the lithologic uniformity, long- and short-term variations in natural gamma radiation and magnetic susceptibility show cyclic alternations that suggest an orbital control of sediment deposition, which will be useful for developing an astrochronology for the sequence. Sites U1513, U1514, U1515, and U1516 were drilled in water depths between 850 and 3900 m in the Mentelle Basin and penetrated 774, 517, 517, and 542 meters below seafloor, respectively. Under a thin layer of Pleistocene to upper Miocene sediment, Site U1513 cored a succession of Cretaceous units from the Campanian to the Valanginian, as well as a succession of basalts. Site U1514 sampled an expanded Pleistocene to Eocene sequence and terminated in the upper Albian. The Cenomanian to Turonian interval at Site U1514 is represented by deformed sedimentary rocks that probably represent a detachment zone. Site U1515 is located on the west Australian margin at 850 m water depth and was the most challenging site to core because much of the upper 350 m was either chert or poorly consolidated sand. However, the prebreakup Jurassic(?) sediments interpreted from the seismic profiles were successfully recovered. Site U1516 cored an expanded Pleistocene, Neogene, and Paleogene section and recovered a complete Cenomanian/Turonian boundary interval containing five layers with high organic carbon content. Study of the well-preserved calcareous microfossil assemblages from different paleodepths will enable generation of paleotemperature and biotic records that span the rise and collapse of the Cretaceous hot greenhouse (including OAEs 1d and 2), providing insight to resultant changes in deep-water and surface water circulation that can be used to test predictions from earth system models. Measurements of paleotemperature proxies and other data will reveal the timing, magnitude, and duration of peak hothouse conditions and any cold snaps that could have allowed growth of a polar ice sheet. The sites contain a record of the mid-Eocene to early Oligocene opening of the Tasman Gateway and the Miocene to Pliocene restriction of the Indonesian Gateway; both passages have important effects on global oceanography and climate. Advancing understanding of the paleoceanographic changes in a regional context will provide a global test on models of Cenomanian to Turonian oceanographic and climatic evolution related both to extreme Turonian warmth and the evolution of OAE 2. The Early Cretaceous volcanic rocks and underlying Jurassic(?) sediments cored in different parts of the Mentelle Basin provide information on the timing of different stages of the Gondwana breakup. The recovered cores provide sufficient new age constraints to underpin a reevaluation of the basin-wide seismic stratigraphy and tectonic models for the region.more » « less
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null (Ed.)The marine-based West Antarctic Ice Sheet (WAIS) is currently locally retreating because of shifting wind-driven oceanic currents that transport warm waters toward the ice margin, resulting in ice shelf thinning and accelerated mass loss. Previous results from geologic drilling on Antarctica’s continental margins show significant variability in ice sheet extent during the late Neogene and Quaternary. Climate and ice sheet models indicate a fundamental role for oceanic heat in controlling ice sheet variability over at least the past 20 My. Although evidence for past ice sheet variability is available from ice-proximal marine settings, sedimentary sequences from the continental shelf and rise are required to evaluate the extent of past ice sheet variability and the associated forcings and feedbacks. International Ocean Discovery Program Expedition 374 drilled a latitudinal and depth transect of five sites from the outer continental shelf to rise in the central Ross Sea to resolve Neogene and Quaternary relationships between climatic and oceanic change and WAIS evolution. The Ross Sea was targeted because numerical ice sheet models indicate that this sector of Antarctica responds sensitively to changes in ocean heat flux. Expedition 374 was designed for optimal data-model integration to enable an improved understanding of Antarctic Ice Sheet (AIS) mass balance during warmer-than-present climates (e.g., the Pleistocene “super interglacials,” the mid-Pliocene, and the Miocene Climatic Optimum). The principal goals of Expedition 374 were to: 1. Evaluate the contribution of West Antarctica to far-field ice volume and sea level estimates; 2. Reconstruct ice-proximal oceanic and atmospheric temperatures to quantify past polar amplification; 3. Assess the role of oceanic forcing (e.g., temperature and sea level) on AIS variability; 4. Identify the sensitivity of the AIS to Earth’s orbital configuration under a variety of climate boundary conditions; and 5. Reconstruct Ross Sea paleobathymetry to examine relationships between seafloor geometry, ice sheet variability, and global climate. To achieve these objectives, postcruise studies will: 1. Use data and models to reconcile intervals of maximum Neogene and Quaternary ice advance and retreat with far-field records of eustatic sea level; 2. Reconstruct past changes in oceanic and atmospheric temperatures using a multiproxy approach; 3. Reconstruct Neogene and Quaternary sea ice margin fluctuations and correlate these records to existing inner continental shelf records; 4. Examine relationships among WAIS variability, Earth’s orbital configuration, oceanic temperature and circulation, and atmospheric pCO2; and 5. Constrain the timing of Ross Sea continental shelf overdeepening and assess its impact on Neogene and Quaternary ice dynamics. Expedition 374 departed from Lyttelton, New Zealand, in January 2018 and returned in March 2018. We recovered 1292.70 m of high-quality core from five sites spanning the early Miocene to late Quaternary. Three sites were cored on the continental shelf (Sites U1521, U1522, and U1523). At Site U1521, we cored a 650 m thick sequence of interbedded diamictite and diatom-rich mudstone penetrating seismic Ross Sea Unconformity 4 (RSU4). The depositional reconstructions of past glacial and open-marine conditions at this site will provide unprecedented insight into environmental change on the Antarctic continental shelf during the late early and middle Miocene. At Site U1522, we cored a discontinuous late Miocene to Pleistocene sequence of glacial and glaciomarine strata from the outer shelf with the primary objective of penetrating and dating RSU3, which is interpreted to reflect the first continental shelf–wide expansion of East and West Antarctic ice streams. Site U1523, located on the outer continental shelf, targeted a sediment drift beneath the westward-flowing Antarctic Slope Current (ASC) to test the hypothesis that changes in ASC vigor regulate ocean heat flux onto the continental shelf and thus ice sheet mass balance. We also cored two sites on the continental rise and slope. At Site U1524, we recovered a Plio–Pleistocene sedimentary sequence from the levee of the Hillary Canyon, one of the largest conduits of Antarctic Bottom Water from the continental shelf to the abyssal ocean. Site U1524 was designed to penetrate into middle Miocene and older strata, but coring was initially interrupted by drifting sea ice that forced us to abandon coring in Hole U1524A at 399.5 m drilling depth below seafloor (DSF). We moved to a nearby alternate site on the continental slope (Site U1525) to core a single hole designed to complement the record at Site U1524. We returned to Site U1524 after the sea ice cleared and cored Hole U1524C with the rotary core barrel system with the intention of reaching the target depth of 1000 m DSF. However, we were forced to terminate Hole U1524C at 441.9 m DSF because of a mechanical failure with the vessel that resulted in termination of all drilling operations and forced us to return to Lyttelton 16 days earlier than scheduled. The loss of 39% of our operational days significantly impacted our ability to achieve all Expedition 374 objectives. In particular, we were not able to recover continuous middle Miocene sequences from the continental rise designed to complement the discontinuous record from continental shelf Site U1521. The mechanical failure also meant we could not recover cores from proposed Site RSCR-19A, which was targeted to obtain a high-fidelity, continuous record of upper Neogene and Quaternary pelagic/hemipelagic sedimentation. Despite our failure to recover a continental shelf-to-rise Miocene transect, records from Sites U1522, U1524, and U1525 and legacy cores from the Antarctic Geological Drilling Project (ANDRILL) can be integrated to develop a shelf-to-rise Plio–Pleistocene transect.more » « less
