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opencc-by-4.0Apr 2020View details →

Flume experiments on the effects of sediment feed rates on step formation, evolution and stability

The dataset contains: - Digital Elevation Models of the experiments collected every hour - Pics of the Bed topography collected every hour - Step number, location, evolution (as described in the paper submitted to Earth Surface Dynamics) - Bed grain-size distribution, sediment and sediment concentration.

opencc-by-4.0Jun 2021View details →

Data for: Faster rates of molecular sequence evolution in reproduction-related genes and in species with hypodermic sperm morphologies

This repository contains a record of analysis scripts and sequence alignments used for the analyses presented in the manuscript. Some of the R scripts depend on supplementary tables associated with the manuscript.

opencc-zeroOct 2019View details →

Data from: Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats, Myotis

Adaptive radiations are defined as rapid diversification with phenotypic innovation led by colonization to new environments. Notably, adaptive radiations can occur in parallel when habitats with similar selective pressures are accessible promoting convergent adaptions. While convergent evolution appears to be a common process, it is unclear what are the main drivers leading the reappearance of morphologies or ecological roles. We explore this question in Myotis bats, the only Chiropteran genus with a worldwide distribution. Three foraging strategies –gleaning, trawling, and aerial netting– repeatedly evolved in several regions of the world, each linked to characteristic morphologies recognized as ecomorphs. Phylogenomic, morphometric, and comparative approaches were adopted to investigate convergence of such foraging strategies and skull morphology as well as factors that explain diversification rates. Genomic and morphometric data were analyzed from ~80% extant taxa. Results confirm that the ecomorphs evolved multiple times, with trawling evolving more often and foliage gleaning most recently. Skull morphology does not reflect common ancestry, evolves convergently with foraging strategy. While diversification rates have been roughly constant across the genus, speciation rates are area-dependent in taxa with temperate distributions. Results suggest that in this species-rich group of bats, first, stochastic processes have led divergence into multiple lineages. Then, natural selection in similar niches has promoted repeated adaptation of phenotypes and foraging strategies. Myotis bats are thus a remarkable case of ecomorphological convergence and an emerging model system for investigating the genomic basis of parallel adaptive radiation.

opencc-by-4.0Feb 2017View details →

Data from Evidence for elevated diversification rate associated with the evolution of active motility in diatoms

These are data files for Evidence for elevated diversification rate associated with the evolution of active motility in diatoms

opencc-zeroOct 2023View details →

Data from: Convergent rates of protein evolution identify novel targets of sexual selection in primates

Sexual selection is the differential reproductive success of individuals, resulting from competition for mates, mate choice, or success in fertilization. In primates, this selective pressure often leads to the development of exaggerated traits which play a role in sexual competition and successful reproduction. In order to gain insight into the mechanisms driving the development of sexually selected traits, we used an unbiased genome-wide approach across 21 primate species to correlate individual rates of protein evolution to relative testes size and sexual dimorphism in body size, two anatomical hallmarks of sexual selection in mammals. Among species with presumed high levels of sperm competition, we detected strong conservation of testes-specific proteins responsible for spermatogenesis and ciliary form and function. In contrast, we identified accelerated evolution of female reproductive proteins expressed in the vagina, cervix, and fallopian tubes in these same species. Additionally, we found accelerated protein evolution in lymphoid tissue, indicating that adaptive immune functions may also be influenced by sexual selection. This study demonstrates the distinct complexity of sexual selection in primates revealing contrasting patterns of protein evolution between male and female reproductive tissues.

opencc-zeroJan 2024View details →

Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales

The macroevolutionary processes that have shaped biodiversity across the temperate realm remain poorly understood and may have resulted from evolutionary dynamics related to diversification rates, dispersal rates, and colonization times, closely coupled with Cenozoic climate change. We integrated phylogenomic, environmental ordination, and macroevolutionary analyses for the cosmopolitan angiosperm family Rhamnaceae to disentangle the evolutionary processes that have contributed to high species diversity within and across temperate biomes. Our results show independent colonization of environmentally similar but geographically separated temperate regions mainly during the Oligocene, consistent with the global expansion of temperate biomes. High global, regional, and local temperate diversity was the result of high in situ diversification rates, rather than high immigration rates or accumulation time, except for Southern China, which was colonized much earlier than other regions. The relatively common lineage dispersals out of temperate hotspots highlights strong source-sink dynamics across the cosmopolitan distribution of Rhamnaceae. The proliferation of temperate environments since the Oligocene may have provided the ecological opportunity for rapid in situ diversification of Rhamnaceae across the temperate realm. Our study illustrates the importance of high in situ diversification rates for the establishment of modern temperate biomes and biodiversity hotspots across spatial scales.

Fig. 8 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises

Fig. 8. Comparison of centrum length/centrum height across Phocoenidae. A. Extinct species: Numataphocoena yamashitai, NFL 7, NMV-5; Pterophocaena nishinoi, NMV-7; Piscolithax longirostris, MNHN SAS 940. B. Extant species: Neophocaena phocaenoides, NMNS M 21382; Phocoenoides dalli, NMNS M 21382; Phocoena phocoena, NMNS M 27393; Phocoena dioptrica, USNM 571486; Phocoena spinipinnis, USNM 550782; Phocoena sinus, NHMUK 69678 (from Noble and Fraser 1971).

Fig. 7. Vertebral character trait evolution across phocoenids and related delphinoids. A. Character 2, thoracic vertebral counts. B. Character 8 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises

Fig. 7. Vertebral character trait evolution across phocoenids and related delphinoids. A. Character 2, thoracic vertebral counts. B. Character 8, ratio of centrum length/centrum height of lumbar vertebrae. C. Character 12, height of neural spine. D. Character 14, regional anterior inclination of neural arches. See Table 2 for detailed character descriptions.

Fig. 5 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises

Fig. 5. The phylogeny and vertebral morphology of Phocoenidae. The phylogenetic analysis is based on the data matrix of Murakami et al. (2012b), excluding character 220, 221, 222, 224, and 227. Quotations added to taxa which are paraphyly or polyphyly in the present cladistic analysis.

Fig. 4 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises

Fig. 4. Vertebrae (A–E) and ribs (F, G) of the porpoise Phocoenidae gen. et sp. indet., NMV-5, early Pliocene of Teshio, Hokkaido, Japan. Cervical (1–7), thoracic (1, 3, 5, 7, X, XX, XXX, last-1, last), and lumbar vertebrae (1–3) in lateral (A) and dorsal (B) views; atlas (C), axis (D), first lumbar (E), left rib fragment (F), and anterior to central right ribs (G) in anterior view.

Fig. 2 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises

Fig. 2. The rostrum (A–D) and mandible (E, F) of the porpoise Phocoenidae gen. et sp. indet., NMV-5, early Pliocene of Teshio, Hokkaido, Japan; in dorsal (A, F), lateral (B, E), ventral (C), and anterior (D) views.

Fig. 3 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises

Fig. 3. Isolated teeth of the porpoise Phocoenidae gen. et sp. indet., NMV-5, early Pliocene of Teshio, Hokkaido, Japan; in buccal view (A, B); longitudinal cross section of B (C); cross section from C stained with Mayer's haematoxylin (D). GLG, growth layer group.

Fig. 1 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises

Fig. 1. The locality of a small porpoise NMV-5. A. The Japanese islands. B. The locality of NMV-5. C. Detailed locality of NMV-5 near the Teshionakagawa area.

Fig. 6 in New fossil remains from the Pliocene Koetoi Formation of northern Japan provide insights into growth rates and the vertebral evolution of porpoises

Fig. 6. Comparisons of the vertebral column of living and extinct phocoenids in lateral view. A. Pterophocaena nishinoi Murakami, Shimada, Hikida, and Hirano, 2012a, late Miocene of Hokkaido, Japan, NMV-7. B. Numataphocoena yamashitai Ichishima and Kimura, 2000, early Pliocene of Hokkaido, Japan, NFL 7. C. Piscolithax aenigmaticus Pilleri and Siber, 1989, late Miocene of Aguada de Lomas of Peru, SMNK-PAL 6660. D. Piscolithax longirostris Muizon, 1983, late Miocene of Sud-Sacaco, → Peru, MNHN SAS 934. E. Neophocaena phocaenoides Cuvier, 1829, Holocene of Japan?, NMNS M 24659. F. Phocoena sinus Norris and McFarland, 1958, Holocene of Baja California, Mexico, LACM 28259. G. Phocoena spinipinnis Burmeister, 1865, Holocene of Peru, USNM 550782. H. Phocoena dioptrica Lahille, 1912, Holocene of Tierra del Fuego, Argentina, LACM 86042. I. Phocoena phocoena Linnaeus, 1758, Holocene of Hokkaido, Japan, NMNS M 27393. J. Phocoenoides dalli True, 1885, Holocene of Iwate, Japan, NMNS M 21382. Not to scale.

opencc-zeroDec 2021View details →

Data for: Faster evolution of a premating reproductive barrier is not associated with faster speciation rates in New World passerine birds

Why are speciation rates so variable across the tree of life? One hypothesis is that this variation is explained by how rapidly reproductive barriers evolve. We tested this hypothesis by conducting a comparative study of the evolution of bird song, a premating barrier to reproduction. Speciation in birds is typically initiated when geographically isolated (allopatric) populations evolve reproductive barriers. We measured the strength of song as a premating barrier between closely related allopatric populations by conducting 2,339 field experiments to measure song discrimination for 175 taxon pairs of allopatric or parapatric New World passerine birds, and estimated recent speciation rates from a global molecular phylogeny of birds. Taxon pairs with high song discrimination in allopatry failed to regularly interbreed in parapatry, evidence that song discrimination is indeed an important reproductive barrier. However, evolutionary rates of song discrimination were not associated with recent speciation rates, and song discrimination evolves faster in suboscine passerines than their more species-rich sister clade, the oscines. Our findings support the long-held idea that song is a key premating reproductive barrier in birds, but show that faster evolution of this reproductive barrier between populations does not result in faster diversification betweeen species.

opencc-by-4.0Apr 2022View details →

Dataset for the paper "Imaging evolution of Cascadia slow‑slip event using high‑rate GPS"

Slip and slip rate files for the preferred model of Itoh, Aoki, and Fukuda (2022, Scientific Reports, doi:10.1038/s41598-022-10957-8). Please see readme.txt for further details. The corresponding author information is also available there. Caution: the dataset has the size of 4.3GB after uncompression/extraction.

opencc-by-4.0Jun 2020View details →

FIGURE 3 in Does soil color affect fish evolution? Differences in color change rate between lineages of the sailfin tetra

FIGURE 3 | A. Representation of the stock tank, with sandy bottom. B. Representation of experimental tank showing the compartments, leaf litter bottom and light bulb. Inner panes: pictures of fish with bright coloration (in stock tank) and dark coloration (after ten minutes of exposure to leaf litter bottom).

opencc-by-4.0Jun 2020View details →

FIGURE 2 in Does soil color affect fish evolution? Differences in color change rate between lineages of the sailfin tetra

FIGURE 2 | Map showing the geographical position of the four populations of Crenuchus spilurus used in this study. Shapes represent the two main lineages that each population represents; squares for the Negro lineage and circles for the Amazonas lineage. Classification of lineages follows Pires et al. (2018).

opencc-by-4.0Jul 2009View details →

Fig. 14 in Neogene radiolarian biostratigraphy and faunal evolution rates in the eastern equatorial Pacific ODP Sites 845 and 1241

Fig. 14. Radiolarians from the early Miocene to Pleistocene of the eastern equatorial Pacific. A. Calocycletta (Calocyclissima) costata (Riedel, 1959). MPC−3324; 845A−26XCC, R19/4; Zone RN5. B. Calocycletta (Calocycletta) robusta Moore, 1971. MPC−3326; 845A−28XCC, Q40/3; Zone RN4. C. Calocycletta (Calocycletta) virginis (Haeckel, 1887). MPC−3326; 845A−28XCC, V46/3; Zone RN4. D. Calocycletta (Calocycletta) cladara Sanfilippo and Riedel, 1992. MPC−3299; 845A−11HCC, K47/4; Zone RN7. E. Calocycletta (Calocyclior) caepa Moore, 1972. MPC−4852; 1241A−30H−07, 62–64 cm, R51/4; Zone RN7. F. Liriospyris reticulata (Ehrenberg, 1872). MPC−3337; 1241A−3H−04, 75–77 cm, Q49/3; Zone RN14. G. Dendrospyris bursa Sanfilippo and Riedel, 1973. MPC−3325; 845A−27XCC, N27/0; Zone RN4. Scale bars 100 µm.