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Fig. 4 in First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens
Fig. 4. Comparison of mitochondrial and nuclear divergence time estimates. A. Chronogram inferred from the mtDNA dataset using BEAST ver. 1.8.4 (Drummond et al. 2012). The mean divergence times are reported on the nodes, and the horizontal grey bars show 95% confidence intervals. B. Phylogram reconstructed from the multispecies coalescent analysis of the nuDNA dataset using *BEAST ver. 2.4.8 (Bouckaert et al. 2014). Divergence times estimated in BEAST ver. 1.8.4 (Drummond et al. 2012) are reported on the nodes to allow comparison with the mtDNA chronogram (Supplementary file 8). Nodes with a white circle were supported by PPBEAST Ż 0.95, whereas nodes with a black circle were supported by both PPBEAST Ż 0.95 and BPML Ż 80.
Fig. 3 in First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens
Fig. 3. Median-joining network of mitochondrial haplotypes. The network was constructed in PopART 1.7 (Leigh & Bryant 2015) based on the mitochondrial sequences of 548 giraffes. The number of mutations between haplotypes is indicated by perpendicular lines on the branches and is specified if greater than 10. The size of the circles is proportional to the number of individuals sharing a certain haplotype with colours assigned by subspecies. The sample locations are indicated by triangles in the map and highlighted in bold capital letters for museum specimens. The subspecies marked with an asterisk represent formerly recognized subspecies, which were synonymized in recent classifications (e.g., Shorrocks 2016). Historical key specimens are highlighted by the respective abbreviation of the museum and the catalogue number.
Fig. 1 in First insights into past biodiversity of giraffes based on mitochondrial sequences from museum specimens
Fig. 1. Distribution range of giraffe subspecies. A. Within historic times (after Dagg 1962). B. At present (after Muller et al. 2018). The subspecies are distinguished by different colours on both maps, whereby the assignment of colours for the nine currently recognized subspecies (B) was modified from https://giraffeconservation.org/giraffe-species/. The type locality for each subspecies is indicated by a triangle in map A and detailed in Table 1.
Figure 2 in The role of female cephalopod researchers: past and present
Figure 2. Female cephalopod scientists. (A) Jeanne (Jeanette) Villepreux-Power (1794–1871). Detail from original photograph taken by A. E. E. Disdéri in 1861. (B) Julia Arsent'evna Filippova (1934- present). (C) Zulma Judith Ageitos de Castellanos (1922–2010). (D) Martina Compagno Roeleveld (1943–2006) (left) with María Edith Ré, currently of the National Patagonic Institute in Puerto Madryn, Argentina (right). Photo taken during the 1997 CIAC meeting in Capetown by Angel Guerra. (E) Nancy A. Voss (1929 – present). (F) Katharina Maria Mangold-Wirz (1922–2003). Photo by Eric Hochberg. (G) Joyce Wells (1930 – present). Photo by Angel Guerra, 1987. (H) Renata Boucher-Rodoni (1942 – present). (I) Eve Boucaud-Camou (1939-present). (J) Marion Nixon (1930 – present). Photo by Angel Guerra, 1992, Aberdeen.
Figure 6 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 6 Strict consensus of two of most parsimonious trees based on morphology. Voucher specimens were chosen from those used in ongoing anchored enrichment molecular analyses. Some taxa were added for better coverage of Tetrastichinae. Unambiguous character state changes are plotted with bars.
Figure 3 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 3 A–F. AKressleinius celans gen. et sp. nov. holotype female, mesosoma, lateral, tps = transepimeral sulcus BAprostocetus hibus, mesosoma, lateral, syn = syntergum CCirrospilus cinctithorax, mesosoma lateral DPnigalio coloni, mesosoma, lateral EAprostocetus hibus, mesosoma dorsal smg = submarginal grooves FNesolynx sp., mesosoma, dorsal.
Figure 2 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 2 A–E. AKressleinius celans gen. et sp. nov., holotype female, fore wing venation, pmv = postmarginal vein, ams = admarginal setae, sms = submarginal vein setae B, CPeckelachertus sp.: B fore wing C habitus DNesolynx sp. habitus EQuadrastichodella sp., habitus.
Figure 1 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 1 A–F.Kressleinius celans gen. et sp. nov., holotype female (SMNS BB-2847) A habitus B habitus, dorsal view, not = notaulus C body, ventral view, pl1 = propleuron D antenna, ocs = ocellar triangle sulcus E mesosoma, lateral, pre = prepectus, tps = transepimeral sulcus F mesosoma, oblique lateral, axl = axillula, pcs = propodeal callus setae, pet = petiole.
Figure 5 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 5 A–D. ASympiesis cf. conica, head, tfs = transfacial sulcus, scs = scrobal sulcus BCrataepus marbis, head, oos = occellar ocular sulcus, ocs = occellar triangle sulcus, uos = upper ocular sulcus CZagrammosoma americanum, mesosoma lateral, pcs = propodeal callus setae DFoersterella erdoesi, mesosoma, lateral.
Figure 4 from: Domer TC, Burks RA, Krogmann L, Heraty JM (2020) Patching up the past one fossil at a time: A new genus and species of Eulophidae from Eocene Baltic Amber (Hymenoptera, Chalcidoidea). Journal of Hymenoptera Research 79: 27-42. https://doi.org/10.3897/jhr.79.55899
Figure 4 A–F. AQuadrastichodella sp., head. F1 = first funicular segment C1 = first clavomere BSympiesis cf. conica, head CBurkseus vittatus, head DNaumanniola sp. head EAprostocetus hibus, mesosoma lateral pcs = propodeal callus setae FDicladocerus westwoodii, mesosoma lateral.
Data from: Does past evolutionary history under different mating regimes influence the demographic dynamics of interspecific competition?
Interspecific interactions are contingent upon organism phenotypes, and thus phenotypic evolution can modify interspecific interactions and affect ecological dynamics. Recent studies have suggested that male-male competition within a species selects for capability to reproductively interfere with a closely related species. Here we examine the effect of past evolutionary history under different mating regimes on the demographic dynamics of interspecific competition in Callosobruchus seed beetles. We used previously established experimental evolution lines of C. chinensis that evolved under either forced lifelong monogamy or polygamy for 17 generations, and examined the demographic dynamics of competition between these C. chinensis lines and a congener, C. maculatus. Callosobruchus chinensis was competitively excluded by C. maculatus in all trials. Time series data analyses suggested that reproductive interference from C. chinensis was relatively more important in the trials involving polygamous C. chinensis than those involving monogamous C. chinensis, in accordance with the potentially higher reproductive interference capability of polygamous C. chinensis. However, the estimated signs and magnitudes of interspecific interactions were not fully consistent with this explanation, implying the evolution of not only reproductive interference but also other interaction mechanisms. Our study thus suggests multifaceted effects of sexually-selected traits on interspecific competitive dynamics.
Data from: Temporal constraints on the potential role of fry odors as cues of past reproductive success for spawning lake trout
Deciding where to reproduce is a major challenge for most animals. Many select habitats based upon cues of successful reproduction by conspecifics, such as the presence of offspring from past reproductive events. For example, some fishes select spawning habitat following odors released by juveniles whose rearing habitat overlaps with spawning habitat. However, juveniles may emigrate before adults begin to search for spawning habitat; hence, the efficacy of juvenile cues could be constrained by degradation or dissipation rates. In lake trout (Salvelinus namaycush), odors deposited by the previous year's offspring have been hypothesized to guide adults to spawning reefs. However, in most extant populations, lake trout fry emigrate from spawning reefs during the spring and adults spawn during the fall. Therefore, we postulated that the role of fry odors in guiding habitat selection might be constrained by the time between fry emigration and adult spawning. Time course chemical, physiological, and behavioral assays indicated that the odors deposited by fry likely degrade or dissipate before adults select spawning habitats. Furthermore, fry feces did not attract wild lake trout to constructed spawning reefs in Lake Huron. Taken together, our results indicate fry odors are unlikely to act as cues for lake trout searching for spawning reefs in populations whose juveniles emigrate before the spawning season, and underscore the importance of environmental constraints on social cues.
Data from: Influences of past climatic changes on historical population structure and demography of a cosmopolitan marine predator, the common dolphin (genus Delphinus)
Climatic oscillations during the Pleistocene have greatly influenced the distribution and connectivity of many organisms, leading to extinctions but also generating biodiversity. While the effects of such changes have been extensively studied in the terrestrial environment, studies focusing on the marine realm are still scarce. Here we used sequence data from one mitochondrial and five nuclear loci to assess the potential influence of Pleistocene climatic changes on the phylogeography and demographic history of a cosmopolitan marine predator, the common dolphin (genus Delphinus). Population samples representing the three major morphotypes of Delphinus were obtained from ten oceanic regions. Our results suggest that short-beaked common dolphins are likely to have originated in the eastern Indo-Pacific Ocean during the Pleistocene and expanded into the Atlantic Ocean through the Indian Ocean. On the other hand, long-beaked common dolphins appear to have evolved more recently and independently in several oceans. Our results also suggest that short-beaked common dolphins had recurrent demographic expansions concomitant with changes in sea surface temperature during the Pleistocene and its associated increases in resource availability, which differed between the North Atlantic and Pacific Ocean basins. By proposing how past environmental changes had an effect on the demography and speciation of a widely distributed marine mammal, we highlight the impacts that climate change may have on the distribution and abundance of marine predators and its ecological consequences for marine ecosystems.
Data from: Inbreeding reveals mode of past selection on male reproductive characters in Drosophila melanogaster
Directional dominance is a prerequisite of inbreeding depression. Directionality arises when selection drives alleles that increase fitness to fixation and eliminates dominant deleterious alleles, while deleterious recessives are hidden from it and maintained at low frequencies. Traits under directional selection (i.e., fitness traits) are expected to show directional dominance and therefore an increased susceptibility to inbreeding depression. In contrast, traits under stabilizing selection or weakly linked to fitness are predicted to exhibit little-to-no inbreeding depression. Here, we quantify the extent of inbreeding depression in a range of male reproductive characters and then infer the mode of past selection on them. The use of transgenic populations of Drosophila melanogaster with red or green fluorescent-tagged sperm heads permitted in vivo discrimination of sperm from competing males and quantification of characteristics of ejaculate composition, performance, and fate. We found that male attractiveness (mating latency) and competitive fertilization success (P2) both show some inbreeding depression, suggesting they may have been under directional selection, whereas sperm length showed no inbreeding depression suggesting a history of stabilizing selection. However, despite having measured several sperm quality and quantity traits, our data did not allow us to discern the mechanism underlying the lowered competitive fertilization success of inbred (f = 0.50) males.
Data from: Learning from the past: a reverberation of past errors in the cerebellar climbing fiber signal
The cerebellum allows us to rapidly adjust motor behavior to the needs of the situation. It is commonly assumed that cerebellum-based motor learning is guided by the difference between the desired and the actual behavior, i.e., by error information. Not only immediate but also future behavior will benefit from an error because it induces lasting changes of parallel fiber synapses on Purkinje cells (PCs), whose output mediates the behavioral adjustments. Olivary climbing fibers, likewise connecting with PCs, are thought to transport information on instant errors needed for the synaptic modification yet not to contribute to error memory. Here, we report work on monkeys tested in a saccadic learning paradigm that challenges this concept. We demonstrate not only a clear complex spikes (CS) signature of the error at the time of its occurrence but also a reverberation of this signature much later, before a new manifestation of the behavior, suitable to improve it.
Data from: Understanding past population dynamics: Bayesian coalescent-based modeling with covariates
Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman's coalescent process enables inference of past population dynamics directly from molecular sequence data, and researchers have developed a number of flexible coalescent-based models for Bayesian nonparametric estimation of the effective population size as a function of time. Major goals of demographic reconstruction include identifying driving factors of effective population size, and understanding the association between the effective population size and such factors. Building upon Bayesian nonparametric coalescent-based approaches, we introduce a flexible framework that incorporates time-varying covariates that exploit Gaussian Markov random fields to achieve temporal smoothing of effective population size trajectories. To approximate the posterior distribution, we adapt efficient Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. Incorporating covariates into the demographic inference framework enables the modeling of associations between the effective population size and covariates while accounting for uncertainty in population histories. Furthermore, it can lead to more precise estimates of population dynamics. We apply our model to four examples. We reconstruct the demographic history of raccoon rabies in North America and find a significant association with the spatiotemporal spread of the outbreak. Next, we examine the effective population size trajectory of the DENV-4 virus in Puerto Rico along with viral isolate count data and find similar cyclic patterns. We compare the population history of the HIV-1 CRF02_AG clade in Cameroon with HIV incidence and prevalence data and find that the effective population size is more reflective of incidence rate. Finally, we explore the hypothesis that the population dynamics of musk ox during the Late Quaternary period were related to climate change.
Data from: Past and present resource availability affect mating rate but not choice in Drosophila melanogaster
The choices of when, where, and with whom to mate represent some of the most important decisions an individual can make to increase their fitness. Several studies have shown that the resources available to an individual during development can dramatically alter their mating rate later in life, and even the choice of mate. However, an individual's surroundings and available resources can change rapidly, and it is not clear how quickly the redistribution of resources towards reproduction can change. To address this important question, we measured mating rate and mate choice among Drosophila melanogaster males that were manipulated in terms of both past resources (control vs. starvation) and the resources available during mate choice (food vs. no food). We found that males given access to ample resources prior to mate choice showed higher mating rates than those that were starved, in agreement with previous studies. However, we also found that this effect can be reversed quickly, as starved males given the opportunity to mate in a high-quality environment mated at frequencies equivalent to their fed counterparts. While past and present resources affected mating rate, they did not affect mate choice, as males mated with high quality females at high frequencies regardless of their condition and environment. Our results show that both current condition as well as the promise of future resources can dramatically influence individuals' investment into reproduction, and that such mating decisions are extremely plastic and reliant on environmental cues.
Data from: The legacy of past human land use in current patterns of mammal distribution
Multiple environmental factors are known to shape species distributions at the global scale, including climate and topography, but understanding current extents of occurrence and biodiversity patterns requires considering anthropogenic factors as well. Numerous studies have explored the relationship between contemporary human activities and different biodiversity metrics, but the influence of past activities, such as land-use, remains poorly understood despite being one of the oldest human impacts. Here we evaluate the role of past land-use modifications in the current distribution and conservation status of mammals worldwide using spatial data characterizing human land use from c.B.C.6000 to c.A.D.2000. First, we applied a clustering method that revealed three generalized past human land-use trajectories that represent low-, recently- and steadily-used areas widely represented across the globe. Second, we fitted boosted regression trees to predict total and threatened mammalian richness, globally and within trajectory-clusters, testing the role of environmental factors and multiple human land-use metrics reflecting: total used area at different time spans, rates of land-use change, and the occurrence of remarkable land-use shifts. Environmental factors were identified as the main correlates of current mammalian richness, but several proposed metrics of past land-use were also relevant predictors. Overall, these results highlight the likely existence of a land-use legacy in some regions of the world that has influenced the distribution of extant mammals, particularly of those currently classified as threatened. Even if we cannot change that legacy, our results show that we need to account for past human impacts to understand present biodiversity patterns and, arguably, to guide future actions.
Data from: Orangutans (Pongo pygmaeus) recognize their own past actions
The ability to recognize oneself in a mirror is known as self-recognition, whereas delayed self-recognition is the ability to recognize the relationship between current self and past actions. While 3-year-old human children have self-recognition without the ability for delayed self-recognition, 4-year-old human children demonstrate the capability for both. Chimpanzees, the most closely related species to humans, have displayed the ability for delayed self-recognition. However, little is known about whether this ability is shared amongst all hominid species. In this study, we examined whether orangutans, the most distantly related species to humans within the hominid group, could recognize their own past actions using the preferential-looking paradigm. Our results demonstrated that orangutans were able to discriminate between a delayed video of themselves presented after a 2-second delay, and a recorded video of the day prior. This suggests that orangutans have the ability to relate their own past actions to current actions, although we found no evidence of self-directed behavior. We believe these findings will contribute to our growing understanding of hominid self-recognition.
Data from: Germ banks affect the inference of past demographic events
Continuous progress in empirical population genetics based on whole genome polymorphism data requires the theoretical analysis of refined models in order to interpret the evolutionary history of populations with adequate accuracy. Recent studies focus prevalently on the aspects of demography and adaptation, whereas age-structure (e.g. in plants via the maintenance of seed banks) has attracted less attention. Germ banking, i.e. seed or egg dormancy, is a prevalent and important life-history trait in plants and invertebrates, which buffers against environmental variability and modulates species extinction in fragmented habitats. Within this study, we investigate the combined effect of germ banking and time-varying population size on the neutral coalescent, and particularly derive the allele frequency spectrum under some simplifying assumptions. We then perform an ABC analysis using two simple demographic scenarios - a population expansion and an instantaneous decline. We demonstrate the appreciable influence of seed banks on the estimation of demographic parameters depending on the germination rate with biases scaled by the square of the germination rate. In the more complex case of a population bottleneck, which comprises an instantaneous decline and an expansion phase, ignoring information on the germination rate denies reliable estimates of the bottleneck parameters via the allelic spectrum. In particular, when seeds remain in the bank over several generations, recent expansions may remain invisible in the frequency spectrum, whereas ancient declines leave signatures much longer than in the absence of seed bank.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.