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3,101 results for “Historical”
Data from: An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the arboreal salamander (Aneides lugubris)
Background: Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus data to reconstruct the evolutionary history of A. lugubris and to discover the geographic location of major genetic breaks within the species. We also used species distribution modeling and comparative phylogeography to better understand the environmental factors that have shaped the genetic history of A. lugubris. Results: We found six major mitochondrial clades in A. lugubris. Nuclear loci supported the existence of at least three genetically distinct groups, corresponding to populations north of the San Francisco Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the central coast and southern California. All of the genetic breaks in mitochondrial and nuclear loci corresponded to regions where historical barriers to dispersal have been observed in other species. Geologic or water barriers likely were the most important factors restricting gene flow among clades. Climatic unsuitability during glacial maximum may have contributed to the isolation of the mitochondrial clades in the central coast and southern California. A projection of our species distribution model to a future scenario with a moderate amount of climate change suggests that most of the range of A. lugubris will remain climatically suitable, but climatic conditions in the Sierra Nevada and low elevation areas in Southern California are likely to deteriorate. Conclusions: Aneides lugubris contains substantial cryptic genetic diversity as a result of historical isolation of populations. At least two (and perhaps three) evolutionarily significant units in A. lugubris merit protection; all six mitochondrial clades should be considered as management units within the species.
Data from: Reconstruction of the historical range alters niche estimates in an endangered rodent
Defining historical baselines is critical for species conservation. Under the niche reduction hypothesis, species in decline may be restricted disproportionately from parts of their environmental niche. This bias likely has important implications for modeling species' distributions if only contemporary occurrences (i.e. post‐range reduction) are used, because suitable habitat will be classified as unsuitable. Unfortunately, robust historical occurrence data is rarely available for sensitive species. In this study, we documented historical locations of the endangered, keystone giant kangaroo rat Dipodomys ingens by examining aerial imagery for burrow mounds. These burrow mounds are readily identifiable and distinguishable from other soil disturbances. We found giant kangaroo rat burrows well outside the currently accepted estimate of their historical distribution. Following the niche reduction hypothesis, we found that giant kangaroo rats have been extirpated from the flattest, hottest, driest parts of their range due to agricultural conversion. This reduction in their realized niche led to significant changes between historical and contemporary models of their distribution. We found that giant kangaroo rats may have occupied up to 56% more habitat historically than currently believed. Our results provide new guidance for managers working on restoration and habitat protection for this ecosystem engineer. This study highlights the critical importance of modeling historical distributions using the entire environmental niche once occupied by species of conservation need.
Data from: Do freshwater ecoregions and continental shelf width predict patterns of historical gene flow in the freshwater fish Poecilia butleri?
We examined historical patterns of gene flow in the freshwater fish Poecilia butleri in western Mexico. We tested the hypothesis that the boundaries between four freshwater ecological communities (ecoregions) might have limited the movement of P. butleri because changes in species compositions might restrict establishment between adjacent ecoregions, even in situations where a physical barrier is absent. Hence, we predicted that boundaries between ecoregions should correspond to phylogeographical breaks in P. butleri. We also tested the hypothesis that the width of the continental shelf affected historical gene flow in P. butleri because a broad continental shelf provides a greater opportunity for rivers to coalesce during historical episodes of low sea levels as opposed to a narrow continental shelf that should restrict the potential for gene flow among adjacent rivers. Hence, we predicted greater amounts of historical gene flow among neighbouring river basins in the region of western Mexico where the continental shelf is wider, whereas, in the region where the continental shelf is narrower, we expected to detect limited levels of historical gene flow. We analyzed mitochondrial DNA sequence data (cytochrome b) taken from 264 individuals of P. butleri collected from 34 locations distributed across four different ecoregions in western Mexico. To examine patterns of phylogenetic diversification and historical gene flow in P. butleri, we employed several analytical approaches, including traditional tree-based phylogenetic analyses (likelihood and parsimony), haplotype network reconstruction, analyses of molecular variance, and spatial analysis of molecular variance. We found genetic breaks coinciding with two out of three different ecoregion boundaries, suggesting limited historical gene flow. In addition to different species compositions between these adjacent ecoregions, geological features such as the Trans-Mexican Volcanic Belt and the mountainous topography in south-western Mexico, likely contributed to these observed genetic breaks. By contrast, no genetic break was evident between two other ecoregions, a result that partially rejects our first hypothesis. Several results were consistent with our second hypothesis. Changes in the width of the continental shelf in western Mexico are associated with the observed patterns of historical gene flow. Our results indicate that the interactions among multiple geological and biological factors affect the spatial patterns of genetic diversity of widespread freshwater species.
Data from: Historical dynamics of ecosystem services bundles
Managing multiple ecosystem services (ES), including addressing trade-offs between services and preventing ecological surprises, is among the most pressing areas for sustainability research. These challenges require ES research to go beyond the currently common approach of snapshot studies limited to one or two services at a single point in time. We used a spatiotemporal approach to examine changes in nine ES and their relationships from 1971 to 2006 across 131 municipalities in a mixed-use landscape in Quebec, Canada. We show how an approach that incorporates time and space can improve our understanding of ES dynamics. We found an increase in the provision of most services through time; however, provision of ES was not uniformly enhanced at all locations. Instead, each municipality specialized in providing a bundle (set of positively correlated ES) dominated by just a few services. The trajectory of bundle formation was related to changes in agricultural policy and global trends; local biophysical and socioeconomic characteristics explained the bundles' increasing spatial clustering. Relationships between services varied through time, with some provisioning and cultural services shifting from a trade-off or no relationship in 1971 to an apparent synergistic relationship by 2006. By implementing a spatiotemporal perspective on multiple services, we provide clear evidence of the dynamic nature of ES interactions and contribute to identifying processes and drivers behind these changing relationships. Our study raises questions about using snapshots of ES provision at a single point in time to build our understanding of ES relationships in complex and dynamic social-ecological systems.
Data from: A population genetic window into the past and future of the walleye Sander vitreus: Relation to historic walleye and the extinct "blue pike" S. v. "glaucus"
Background: Conserving genetic diversity and local adaptations are management priorities for wild populations of exploited species, which increasingly are subject to climate change, habitat loss, and pollution. These constitute growing concerns for the walleye Sander vitreus, an ecologically and economically valuable North American temperate fish with large Laurentian Great Lakes' fisheries. This study compares genetic diversity and divergence patterns across its widespread native range using mitochondrial (mt) DNA control region sequences and nine nuclear DNA microsatellite (μsat) loci, examining historic and contemporary influences. We analyze the genetic and morphological characters of a putative endemic variant– "blue pike" S. v. "glaucus" –described from Lakes Erie and Ontario, which became extinct. Walleye with turquoise-colored mucus are evaluated, since some have questioned whether these are related to the "blue pike". Results: Walleye populations are distinguished by significant considerable genetic divergence (mean FST mtDNA=0.32±0.01, μsat=0.13±0.00) and substantial diversity across their range (mean heterozygosity mtDNA=0.53±0.02, μsat=0.68±0.03). Southern populations markedly differ, possessing unique haplotypes and alleles, especially the . The Ohio/New River population that housespossesses the most pronounced divergence and the oldest haplotype. Northerly formerly glaciated populations have greatest diversity in Lake Erie (mean heterozygosity mtDNA=0.79±0.00, μsat=0.72±0.01). Genetic diversity was much less in historic Lake Erie samples from 1923–1949 (mean heterozygosity mtDNA=0.05±0.01, μsat=0.47±0.06) than today. The historic "blue pike" had no unique haplotypes/alleles and there is no evidence that it comprised a separate taxon from walleye. Turquoise mucus walleye also show no genetic differentiation from other sympatric walleye and no correspondence to the "blue pike". Conclusions: Contemporary walleye populations possess high levels of genetic diversity and divergence, despite habitat degradation and exploitation. Genetic and previously published tagging data indicate that natal homing and spawning site philopatry led to population structure. Population patterns were shaped by climate change and drainage connections, with northern ones tracing to post-glacial recolonization. Southerly populations possess unique alleles and may provide an important future genetic reservoir. Allelic frequencies of Lake Erie walleye from ~70–90 years ago significantly differed from today, suggesting population recovery after extensive habitat loss, pollution, and exploitation. The historic "blue pike" was indistinguishable from walleye, indicating that taxonomic designation is not warranted.
Data from: Conservation of old individual trees and small populations is integral to maintain species' genetic diversity of a historically fragmented woody perennial
Historically fragmented and specialised habitats such as granite outcrops are understudied globally unique hotspots of plant evolution. In contrast to predictions based on mainstream population genetics theory, some granite outcrop plants appear to have persisted as very small populations despite prolonged geographic and genetic isolation. Eucalyptus caesia Benth. is a long-lived lignotuberous tree endemic with a naturally fragmented distribution on granite outcrops in south-western Australia. To quantify population to landscape level genetic structure we employed microsatellite genotyping at 14 loci of all plants in 18 stands of E. caesia. Sampled stands were characterised by low levels of genetic diversity, small absolute population sizes, localised clonality and strong fine-scale genetic sub-division. There was no significant relationship between population size and levels of heterozygosity. At the landscape scale, high levels of population genetic differentiation were most pronounced among representatives of the two subspecies in E. caesia as originally circumscribed. Past genetic interconnection was evident between some geographical neighbours separated by up to 20 kilometres. Paradoxically, other pairs of neighbouring stands as little as 7 kilometres apart were genetically distinct. There was no consistent pattern of isolation by distance across the 280 km range of E. caesia. Low levels of gene flow, together with strong drift within stands, provides some explanation of the patterns of genetic differentiation we observed. Individual genet longevity via the ability to repeatedly re-sprout and expand from a lignotuber may enhance the persistence of some woody perennial endemic plants despite small population size, minimal genetic interconnection and low heterozygosity.
Maintaining historic disturbance regimes increases species' resilience to catastrophic hurricanes
<p>As habitat loss and fragmentation, urbanization, and global climate change accelerate, conservation of rare ecosystems increasingly relies on human intervention. However, any conservation strategy is vulnerable to unpredictable, catastrophic events. Whether active management increases or decreases a system's resilience to these events remains unknown. Following Hurricane Irma's landfall in our habitat restoration study sites, we found that rare ecosystems with active, human-imposed management suffered less damage in a hurricane's path than unmanaged systems. At the center of Irma's landfall, we found Croton linearis' (a locally rare plant that is the sole host for two endangered butterfly species) survival and population growth rates in the year of the hurricane were higher in previously managed plots than in un-managed controls. In the periphery of Irma's circulation, the effect of prior management was stronger than that of the hurricane. Maintaining the historical disturbance regime thus increased the resilience of the population to major hurricane disturbance. As climate change increases the probability and intensity of severe hurricanes, human management of disturbance-adapted landscapes will become increasingly important for maintaining populations of threatened species in a storm's path. Doing nothing will accelerate extinction.</p>
Data from: Multiplex preamplification PCR and microsatellite validation allows accurate single nucleotide polymorphism (SNP) genotyping of historical fish scales
Incorporating historical tissues into the study of ecological, conservation, and management questions can broaden the scope of population genetic research by enhancing our understanding of evolutionary processes and anthropogenic influences on natural populations. Genotyping historical and low-quality samples has been plagued by challenges associated with low amounts of template DNA and the potential for preexisting DNA contamination among samples. We describe a two-step process designed to (i) accurately genotype large numbers of historical low-quality scale samples in a high-throughput format and (ii) screen samples for preexisting DNA contamination. First, we describe how an efficient multiplex preamplification PCR of 45 single nucleotide polymorphisms (SNPs) can generate highly accurate genotypes with low failure and error rates in subsequent SNP genotyping reactions of individual historical scales from sockeye salmon (Oncorhynchus nerka). Second, we demonstrate how the method can be modified for the amplification of microsatellite loci to detect preexisting DNA contamination. A total of 760 individual historical scale and 182 contemporary fin clip samples were genotyped and screened for contamination. Genotyping failure and error rates were exceedingly low and similar for both historical and contemporary samples. Preexisting contamination in 21% of the historical samples was successfully identified by screening the amplified microsatellite loci. The potential for automation, low failure and error rates, and ability to multiplex both the preamplification and subsequent genotyping reactions combine to make the protocol ideally suited for efficiently genotyping large numbers of potentially contaminated low-quality sources of DNA.
Figure 10 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 10. Mantidactylus (Mantidactylus) radaka sp. nov. being prepared for human consumption. (a) Frogs and crabs are collected from broad streams. Then (b) the frogs are gutted and skinned, and the head, hands and feet removed. The frog is then rinsed in the stream, leaving (c) cleaned animals for cooking in a stew. Note the ovaries full with hundreds of eggs.
Figure 9 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 9. Preserved type specimens of the four nomina in the Mantidactylus subgenus Mantidactylus and one of the paralectotypes of Rana guttulata.
Figure 7 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 7. Photographs of living specimens of Mantidactylus (Mantidactylus) guttulatus, M. (M.) grandidieri, and of three candidate species. (a, b) M. (M.) guttulatus, female ZSM 1013/2003 (FGMV 2002.438) from Ranomafana. (c) Unidentified specimen from Ranomafana, assigned tentatively to M. (M.) guttulatus (no genetic evidence). (d, e) M. (M.) guttulatus, specimen KU 340853 (CRH729) from Ranomafana. (f) M. (M.) grandidieri, specimen ZSM 5077/2005 (ZCMV 2159) from Nosy Mangabe. (g) M. (M.) grandidieri, specimen ZSM 276/2005 (FGZC 2682) from Vohidrazana. (h) M. (M.) grandidieri, unidentified specimen (probably subadult) from Andranofotsy. (i, j) M. (M.) grandidieri, specimen KU
Figure 5. Per-base coverage plots for the 16S in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 5. Per-base coverage plots for the 16S fragment in four Mantidactylus type specimens from the MNHN and BMNH collections. (a) BMNH 1947.2.25.48 (paralectotype of Rana guttulata); (b) BMNH 1947.2.25.51 (paralectotype of Rana guttulata); (c) MNHN 1895.255 (syntype of M. grandidieri); (d) MNHN 1883.520 (syntype of M. grandidieri).
Figure 3 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 3. Haplotype network of the subgenus Mantidactylus based on 1227 bp of the nuclear RAG-1 gene from 39 samples. Small black dots represent additional mutational steps.
Figure 2 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 2. Diagonal matrix visualising the mean uncorrected genetic distances (p-distances) in the mitochondrial 16S rRNA gene between the different lineages in the subgenus Mantidactylus, calculated from 514 bp of the 16S mitochondrial gene.
Figure 1. Maximum likelihood phylogenetic tree obtained from 514 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 1. Maximum likelihood phylogenetic tree obtained from 514 bp of the mitochondrial 16S rRNA gene. The values at the nodes are the bootstrap supports (not given for intra-lineage nodes for improved clarity). The type specimens of M. guttulatus and M. grandidieri from the London and Paris museum collections are highlighted in red and brown, respectively.
Figure 4 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 4. Stacked barplots showing the number of reads uniquely matching different reference sequences for the three targeted mitochondrial genes with a similarity threshold of 98%. The Rana pigra type was not included because the number of reads was too low.
Figure 8 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 8. Lateral views of the heads of preserved adult males of Mantidactylus (Mantidactylus) radaka sp. nov. in comparison with M. (M.) guttulatus and M. (M.) grandidieri. Note the more distinct and larger tympanum (indicated by yellow arrows) in the latter two species. Not to scale.
Figure 6 in Target-enriched DNA sequencing from historical type material enables a partial revision of the Madagascar giant stream frogs (genus Mantidactylus)
Figure 6. Photographs of living specimens of Mantidactylus radaka sp. nov. (a, b) Male holotype ZSM 644/2001 (field number FGMV 2001.132) from Manarikoba forest, Tsaratanana Massif. (c–f) Female paratype ZSM 1800/2010 (ZCMV 12345) from Camp 1 (Antevialambazaha), Tsaratanana Massif. (g, h) Female paratype ZSM 97/2016 (MSZC 0080) from Ampotsidy. (i, j) Male paratype MSZC 0120 (uncatalogued in UADBA) from Ampotsidy. (k) Unidentified specimen from Camp 0 (Ankijagna Lagnana), Tsaratanana Massif. (l) Paratype ZSM 582/2014 (DRV 6073) from Camp 0 (Ankijagna Lagnana). (m, n) Unidentified female specimen from Manongarivo (Camp 0), probably preserved in UADBA collection.
Historic Pot [Photogrammetry]
Historic Pot photogrammetry done using KIRI Engine on an iphoneX. Source: Objaverse 1.0 / Sketchfab
Historic stapler
Scan using a Canon EOS 5DsR and Agisoft PhotoScan Source: Objaverse 1.0 / Sketchfab
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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)
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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.
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