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Data from: Historic and contemporary use of catfish aquaculture by piscivorous birds in the Mississippi Delta
<p>This dataset contains data used in the manuscript "Historic and contemporary use of catfish aquaculture by piscivorous birds in the Mississippi Delta", published in The Condor: Ornithological Applications. All data were collected in northwest Mississippi during winters (October - April) of 2000-2001, 2003-2004, 2015-2016, 2016-2017, and 2017-2018. Two primary types of data are present: 1) roost surveys, and 2) aquaculture cluster surveys. Roost surveys were aerial surveys in which all known double-crested cormorant night roosts in northwest Mississippi were surveyed and cormorants were counted. Roost survey data can be found in the "Cormorant_Roost_Survey_Counts.xlxs" file. For the aquaculture cluster surveys, clusters were defined as U.S. Geological Survey land survey sections that contained aquaculture. For each year of data, a random subset of these clusters were chosen to be aerial surveyed and double-crested cormorants, great blue herons, and great egrets were recorded per cluster. Basic descriptive statistics of the clusters can be found in the "Cluster_Descriptive_Stats.xlxs" file. The "Historic_vs_Contemporary_Cormorants.xlxs" file was used to compare cormorant density on aquaculture clusters between the historic period (2000-2001, 2003-2004) and contemporary period (2015-2016, 2016-2017, and 2017-2018). Lastly, the "Cluster_Survey_Data_Contemporary.xlxs" file contains data recorded during the contemporary period only, and other variables regarding the clusters are also present.</p>
FIGURE 6 in Biogeography of Glandulocaudinae (Teleostei: Characiformes: Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity
FIGURE 6. Spermann correlation between average genetic distances (GTR) and geographic distances showing no statistical support among variables.
FIGURE 5 in Biogeography of Glandulocaudinae (Teleostei: Characiformes: Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity
FIGURE 5. Bayesian cladogram showing the phylogentic relationships among populations of Mimagoniates microlepis from SE and S Brazil. Orange branches represent samples from rio Iguaçu basin. Blue branches represent streams from the coastal area. Numbers in branches indicates the posterior probabilities of the clusterings for GTR distances, obtained by Monte Carlo Markov Chains. Sampled localities are the follow: PIR= rio Piraquara, Piraquara, state of Paraná; CAE= rio Caerana, Piraquara, state of Paraná; PEQ= rio Pequeno, São José dos Pinhais, state of Paraná; VAR= rio da Várzea, Lapa, state of Paraná; AGU= rio Água Verde, Canoinhas, state of Santa Catarina; MER= rio Mergulhão, Antonina, state of Paraná; RIB= rio Ribeirão, Paranaguá, state of Paraná; MON= rio Mongaguá, Mongaguá, state of São Paulo; ITA= rio Caixa d'Água, Itariri, state of São Paulo; ACA= tributary of rio Acaraí, São Francisco do Sul, state of Santa Catarina. For each locality, 10 specimens were sampled and are indicated by numbers 0-9.
FIGURE 3. A in Biogeography of Glandulocaudinae (Teleostei: Characiformes: Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity
FIGURE 3. A) Distribution of the Glandulocaudinae and the topographic and tectonic features of SE South America. Double lines corresponds to the main axes of Quaternary tectonics in the area (according to Saadi, 1993; Saadi et al., 2002 and Riccomini et al. 2001) B) The same area showed within the contest of major tectonic provinces of South American Platform. I – South American Platform; II – Patagonian massif; III – Andean orogenic belt; IV – foreland basins; AM = Amazon craton; SL = São Luis craton; SF = São Francisco craton; LA = Luiz Alves craton; RP = Rio de la Plata craton; B = Borborema province; T = Tocantins province; M = Mantiqueira province; DF = Dom Feliciano belt. (Modified from Cordani et al., 2000).
FIGURE 1 in Biogeography of Glandulocaudinae (Teleostei: Characiformes: Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity
FIGURE 1. Representatives of the Glandulocaudinae and their caudal organs. A) Lophiobrycon weitzmani; paratype, LIRP 4338, photo by R.M.C. Castro; B) Glandulocauda melanogenys, uncatalogued specimens, collected at Estação Biológica de Boracéia, Rio Guaratuba basin, photo by J.C. Nolasco C) Mimagoniates microlepis, photo by R.L. Corte. Arrows indicate the caudal-fin rays 11 and 12. (modified from Menezes & Weitzman, 1990 and Castro et al. 2003).
Data from: High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements
Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27–43). On average, 66.2% of the reads mapped to the pseudo-reference genome of each species. Of these mapped reads, an average of 52.7% was identified as PCR or optical duplicates. We achieved deeper effective sequencing for historical samples (122.7×) compared to modern samples (23.5×). The number of nucleotide sites with at least 8× sequencing depth was high, with averages ranging from 0.89 × 106 bp (Arachnothera, modern samples) to 1.98 × 106 bp (Stachyris, modern samples). Linear regression revealed that the amount of sequence data obtained from each historical sample (represented by per cent of the pseudo-reference genome recovered with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013) related to how recently the sample was collected. We observed characteristic post-mortem damage in the DNA of historical samples. However, we were able to reduce the error rate significantly by truncating ends of reads during read mapping (local alignment) and conducting stringent SNP and genotype filtering.
FIGURE 1 in Ants of the State of Pará, Brazil: a historical and comprehensive dataset of a key biodiversity hotspot in the Amazon Basin
FIGURE 1. Ant sampling distribution (localities) in the state of Pará by data source (A), area of endemism (B), vegetation type (C), protected area (D), roads and rivers (E), and the distribution of exotic ants in 78 records (F). DF = Dense Ombrophilous Forest; OF = Open Ombrophilous Forest; DcF = Seasonal Deciduous Forest; SF = Secondary Forest; PV = Pioneer Vegetation; VR = Refúgio Vegetacional; Sv = Savanna.
FIGURE 4 in Ants of the State of Pará, Brazil: a historical and comprehensive dataset of a key biodiversity hotspot in the Amazon Basin
FIGURE 4. Collector's curve based on museum specimens (546 species) and published sources (561 species) for ant species recorded in the state of Pará, Brazil, between 1886 and 2018.
FIGURE 2 in Ants of the State of Pará, Brazil: a historical and comprehensive dataset of a key biodiversity hotspot in the Amazon Basin
FIGURE 2. Abundance distribution of site-specific ant species records in the state of Pará. The x-axis is on a logarithmic scale.
FIGURE 3 in Ants of the State of Pará, Brazil: a historical and comprehensive dataset of a key biodiversity hotspot in the Amazon Basin
FIGURE 3. Number of ant records in the state of Pará based on museum specimens and published sources over time. Note: 695 of 3,502 site-specific records from published sources did not indicate the collection year; 64 of 4,531 site-specific records from museum specimens did not indicate the collection year.
Strolling through a century: replicating historical bird surveys to explore 100 years of change in an urban bird community
<p>In 1898, Herbert and Alice Walter started a 5-year survey of birds in Lincoln Park, – the largest park in Chicago, IL – and summarized their data in an urban birding field guide, 'Wild Birds in City Parks'. Twenty-nine years later, William Dreuth compared the relative frequency of species between the Walter's study to their own 5-year Lincoln Park survey. Between 2012 and 2015, we replicated these surveys to investigate a century of bird diversity and community composition change in urban Chicago. While species richness did not change, community composition did. We found that 1) species with a greater diet breadth and 2) species that increased in statewide occupancy were more likely to increase in frequency over time. We conclude that factors at multiple scales brought temporal changes to Chicago's bird community. Overall, this survey highlights the slow and subtle ways in which species may respond to a century of urban intensification.</p>
Is phylogeographic congruence predicted by historical habitat stability, or ecological co-associations?
<p>Comparative phylogeographic studies can uniquely distinguish idiosyncratic versus community-wide responses to past environmental change. However, to date, impacts of species interactions have been largely overlooked. Here we used non-genetic data to characterize two competing scenarios about expected levels of congruence among five saproxylic invertebrate species (i.e., a wood-feeding cockroach, termite and beetle; a predatory centipede, and a detritivorous millipede) from the southern Appalachians mountains—a topographically complex unglaciated landscape. Under one scenario, abiotic factors primarily drove species' responses, with predicted congruence based on spatial overlap of climatically stable habitat areas estimated for each species via ecological niche modeling. The other scenario considered biotic factors to be most influential, with proxies for actual or potential direct interactions used to predict congruence. Analyses of mitochondrial and nuclear DNA sequence datasets for each species focused on four axes of comparison: the number and distribution of spatial-genetic clusters, phylogeographic structure, changes in long-term effective population size, and historical gene flow dynamics. Overall, we found stronger support for ecological co-associations scenario, suggesting an important influence of biotic factors in constraining or facilitating species' responses to Pleistocene climatic cycles. However, there was an imperfect fit between this scenario's predictions and outcomes of empirical data analyses. Thus, our conclusions are compelling, but tentative. This work advances comparative phylogeography by expanding the scope of inferences beyond abiotic drivers, and provides insights into the evolutionary history of a functionally important ecological community, within a globally recognized center of endemism.</p>
FIGURE 1 in Typification of Pascalia glauca (Heliantheae, Asteraceae), with historical notes on that name
FIGURE 1. Pascalia glauca Ortega. Lectotype (iconotype), engraving by I. Gálvez in Gómez-Ortega (1797: tab. 4). Reproduced with permission (Biblioteca, Real Jardín Botánico de Madrid).
FIGURE 2 in Typification of Pascalia glauca (Heliantheae, Asteraceae), with historical notes on that name
FIGURE 2. Pascalia glauca Ortega. Epitype (MA-244280, the fragment on the upper right side). Reproduced with permission (MA, Real Jardín Botánico de Madrid).
FIGURE 3 in Typification of Pascalia glauca (Heliantheae, Asteraceae), with historical notes on that name
FIGURE 3. Living plants of Pascalia glauca Ortega growing in the Real Jardín Botánico de Madrid (MA). A: Lower leaf; B: Flowering head; C: Details of the involucre; D: Fruiting head. Photographs by Carlos Aedo (personal collection num. CA 19537).
Data from: Unraveling historical introgression and resolving phylogenetic discord within Catostomus (Osteichthys: Catostomidae)
Background: Porous species boundaries can be a source of conflicting hypotheses, particularly when coupled with variable data and/or methodological approaches. Their impacts can often be magnified when non-model organisms with complex histories of reticulation are investigated. One such example is the genus Catostomus (Osteichthys, Catostomidae), a freshwater fish clade with conflicting morphological and mitochondrial phylogenies. The former is hypothesized as reflecting the presence of admixed genotypes within morphologically distinct lineages, whereas the latter is interpreted as the presence of distinct morphologies that emerged multiple times through convergent evolution. We tested these hypotheses using multiple methods, to including multispecies coalescent and concatenated approaches. Patterson's D-statistic was applied to resolve potential discord, examine introgression, and test the putative hybrid origin of two species. We also applied naïve binning to explore potential effects of concatenation. Results: We employed 14,007 loci generated from ddRAD sequencing of 184 individuals to derive the first highly supported nuclear phylogeny for Catostomus. Our phylogenomic analyses largely agreed with a morphological interpretation,with the exception of the placement of Xyrauchen texanus, which differs from both morphological and mitochondrial phylogenies. Additionally, our evaluation of the putative hybrid species C. columbianus revealed a lack introgression and instead matched the mitochondrial phylogeny. Furthermore, D-statistic tests clarified all discrepancies based solely on mitochondrial data, with agreement among topologies derived from concatenation and multispecies coalescent approaches. Extensive historic introgression was detected across six species-pairs. Potential endemism in the Virgin and Little Colorado Rivers was also apparent, and the former genus Pantosteus was derived as monophyletic, save for C. columbianus. Conclusions: Complex reticulated histories detected herein support the hypothesis that introgression was responsible for conflicts that occurred within the mitochondrial phylogeny, and explains discrepancies found between it and previous morphological phylogenies. Additionally, the hybrid origin of C. columbianus was refuted, but with the caveat that more fine-grain sampling is still needed. Our diverse phylogenomic approaches provided largely concordant results, with naïve binning useful in exploring the single conflict. Considerable diversity was found within Catostomus across southwestern North America, with two drainages [Virgin River (UT) and Little Colorado River (AZ)] reflecting unique composition.
Historical warming consistently decreased size, dispersal and speciation rate of fish
<p>There is ongoing debate as to whether fish body size will decrease with global warming and how these changes may impact dispersal ability and speciation rate. Theory predicts that, under warmer temperatures, fish grow to a smaller size, undergo a reduction in dispersal ability and increase speciation rates. However, evaluations of such predictions are hampered owing to the lack of empirical data spanning both wide temporal and geographical scales. Here, using phylogenetic methods, we show that smaller clupeiform fish (anchovies and herrings) occurred historically in warmer waters, moved the shortest distances at low speed and displayed the lowest speciation rates. Furthermore, fish moved faster and evolved rapidly under higher rates of temperature change but these historical rates are far lower than current warming rates. Our results predict a future where smaller clupeiform fish that have reduced ability to move will be more prevalent; this, in turn, may reduce future speciation.</p>
Presence, precipitation, and temperature data used to estimate eastern forest songbird historical distributions using climatic niche modeling
<p>Boundaries between vegetation types, known as ecotones, can be dynamic in response to climatic changes. The North American Great Plains includes a forest-grassland ecotone in the south-central United States that has expanded and contracted in recent decades in response to historical periods of drought and pluvial conditions. This dynamic region also marks a western distributional limit for many passerine birds that typically breed in forests of the eastern United States. To better understand the influence that variability can exert on broad-scale biodiversity, we explored historical longitudinal shifts in the western extent of breeding ranges of eastern forest songbirds in response to the variable climate of the southern Great Plains. We used climatic niche modeling to estimate current distributional limits of nine species of forest-breeding passerines from 30-year average climate conditions from 1980 to 2010. During this time the southern Great Plains experienced an unprecedented wet period without periodic multi-year droughts that characterized the region's long-term climate from the early 1900s. Species' climatic niche models were then projected onto two historical drought periods: 1952–1958 and 1966–1972. Threshold models for each of the three time periods revealed dramatic breeding range contraction and expansion along the forest-grassland ecotone. Precipitation was the most important climate variable defining breeding ranges of these nine eastern forest songbirds. Range limits extended farther west into southern Great Plains during the more recent pluvial conditions of 1980–2010 and contracted during historical drought periods. An independent dataset from BBS was used to validate 1966–1972 range limit projections. Periods of lower precipitation in the forest-grassland ecotone are likely responsible for limiting the western extent of eastern forest songbird breeding distributions. Projected increases in temperature and drought conditions in the southern Great Plains associated with climate change may reverse range expansions observed in the past 30 years.</p>
Figure 5 in Historical perspective, new contributions and an enlightening dispersal mechanism for the endogean genus Typhlocharis Dieck 1869 (Coleoptera: Carabidae: Trechinae)
Figure 5. Hypothetical relationships within the Typhlocharis species with unguiform and tubular gonocoxites. (A) Hypothesis 1; (B) hypothesis 2; (C) hypothesis 3; (D) hypothesis 4.
Figure 1 in Historical perspective, new contributions and an enlightening dispersal mechanism for the endogean genus Typhlocharis Dieck 1869 (Coleoptera: Carabidae: Trechinae)
Figure 1. Trends in the description of Typhlocharis and other endogean environment captured species of Anillini. Lines represent the respective accumulation curves.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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