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opencc-zeroApr 2015View details →

Model, data, and analysis for Negative Niche Construction Favors the Evolution of Cooperation

This repository contains the model, data, and analysis corresponding to Negative Niche Construction Favors the Evolution of Cooperation as submitted for review by Brian D. Connelly, Katherine J. Dickinson, Sarah P. Hammarlund, and Benjamin Kerr. Contents are released to the public domain under the Creative Commons CC0 License.

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Vibroscape analysis reveals acoustic niche overlap and plastic alteration of vibratory courtship signals in ground-dwelling wolf spiders

Soundscape ecology has enabled researchers to investigate natural interactions among biotic and abiotic sounds as well as their influence on local animals. To expand the scope of soundscape ecology to encompass substrate-borne vibrations (i.e. vibroscapes), we developed methods for recording and analyzing sounds produced by ground-dwelling arthropods to characterize the vibroscape of a deciduous forest floor using inexpensive contact microphone arrays followed by automated sound filtering and detection in large audio datasets. Through the collected data, we tested the hypothesis that closely related species of Schizocosa wolf spider partition their acoustic niche. In contrast to previous studies on acoustic niche partitioning, two closely related species - S. stridulans and S. uetzi - showed high acoustic niche overlap across space, time, and/or signal structure. Finally, we examined whether substrate-borne noise, including anthropogenic noise (e.g., airplanes) and heterospecific signals, promotes behavioral plasticity in signaling behavior to reduce the risk of signal interference. We found that all three focal Schizocosa species increased the dominant frequency of their vibratory courtship signals in noisier signaling environments. Also, S. stridulans males displayed increased vibratory signal complexity with an increased abundance of S. uetzi, their sister species with which they are highly overlapped in the acoustic niche.

opencc-zeroFeb 2024View details →

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Data for: Range and niche expansion through multiple interspecific hybridization - a genotyping by sequencing analysis of Cherleria (Caryophyllaceae)

Background: Cherleria (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was identified using nuclear ribosomal (nrDNA) sequence data in a previous study. With the nrDNA data, all but one species was monophyletic, with little sequence variation within most species. Here, we use genotyping by sequencing (GBS) data to determine whether the nrDNA data showed the full picture of the evolution in the genomes of these species. Results: The overall relationships found with the GBS data were congruent with those from the nrDNA study. Most of the species were still monophyletic and many of the same subclades were recovered, including a clade of three narrow endemic species from Greece and a clade of largely calcifuge species. The GBS data provided additional resolution within the two species with the best sampling, C. langii and C. laricifolia, with structure that was congruent with geography. In addition, the GBS data showed significant hybridization between several species, including species whose ranges did not currently overlap. Conclusions: The hybridization led us to hypothesize that lineages came in contact on the Balkan Peninsula after they diverged, even when those lineages are no longer present on the Balkan Peninsula. Hybridization may also have helped lineages expand their niches to colonize new substrates and different areas. Not only do genome-wide data provide increased phylogenetic resolution of difficult nodes, they also give evidence for a more complex evolutionary history than what can be depicted by a simple, branching phylogeny.

opencc-zeroJun 2022View details →

Figure 5 in Analysis of the spatial organization of Vallonia pulchella (Muller, 1774) ecological niche in Technosols (Nikopol manganese ore basin, Ukraine)

Figure 5. Correlation between the environment variables and the axes selected as a result of FANTER analysis. A – marginality axes 1 and 2; B - specialization axes 44 and 45. Type_1 - type_6 - the proportion of physiognomic types of vegetation cover; temp_05 - top soil temperature (3-5 cm) May 3, 2012; temp_06 - temperature of the top layer of soil (3-5 cm) June 20, 2012; Tm - thermoclimate; Kn - continentality; Om - ombroclimate; Kr - cryoclimate; Hd - humidity; Tr - salt regime; Nt - nitrogen nutrition; Rc - acidity; Lc - lighting; St - stepants; Pr - pratants; Humus – humus comtant; EC – soil electrical conductivity, imp_05 - imp_50 - soil mechanical impedance at a depth of 5, ..., 50 cm, Agr_10 - Agr_025 - aggregate fractions of size> 10, ..., <0.25 mm, g_Vlag - hygroscopic humidity,%; Compact – soil shrinkage, in %.

Figure 8 in Analysis of the spatial organization of Vallonia pulchella (Muller, 1774) ecological niche in Technosols (Nikopol manganese ore basin, Ukraine)

Figure 8. Spatial distribution of the habitat preference index (HSI) for Vallonia pulchella within the experimental site on red-brown clays based on ENFA (top) and MADIFA (bottom) procedures. The arrow indicates the zones of greatest difference.

Figure 4 in Analysis of the spatial organization of Vallonia pulchella (Muller, 1774) ecological niche in Technosols (Nikopol manganese ore basin, Ukraine)

Figure 4. An histogram of the available resource units. Resource allocation (black bars) and an histogram of the used resource units distribution of resource use (gray bars) of Vallonia pulchella. Type_1 - type_6 - the proportion of physiognomic types of vegetation cover; temp_05 - top soil temperature (3-5 cm) May 3, 2012; temp_06 - temperature of the top layer of soil (3-5 cm) June 20, 2012; Tm - thermoclimate; Kn - continentality; Om - ombroclimate; Kr - cryoclimate; Hd - humidity; Tr - salt regime; Nt - nitrogen nutrition; Rc - acidity; Lc - lighting; St - stepants; Pr - pratants; Humus – humus comtant; EC – soil electrical conductivity, imp_05 - imp_50 - soil mechanical impedance at a depth of 5, ..., 50 cm, Agr_10 - Agr_025 - aggregate fractions of size> 10, ..., <0.25 mm, g_Vlag - hygroscopic humidity,%; Compact – soil shrinkage, in %.

Figure 2 in Analysis of the spatial organization of Vallonia pulchella (Muller, 1774) ecological niche in Technosols (Nikopol manganese ore basin, Ukraine)

Figure 2. Soil surface and physiognomic characteristics of the vegetation cover. 1 – type_1 (Bromus sguarrosus L.); 2 – type_2 (Seseli tortuosum L.); 3 – type_3 (Lactuca tatarica (L.) C.A. Mey.); 4 – type_4 (Medicago sativa L.); 5 – type_5 (dead plant residue); 6 – type_6 (open soil cover).

Figure 1 in Analysis of the spatial organization of Vallonia pulchella (Muller, 1774) ecological niche in Technosols (Nikopol manganese ore basin, Ukraine)

Figure 1. Research Centre of the Dnipro Agrarian and Economic University in Pokrov (Ukraine). A – satellite image of the study area (1 – reclaimed land; 2 – mining quarry); B – technosoils profile; C – quarry panorama view.

Fig. 3 in Investigating the pathogens associated with Dermacentor nuttalli and its global distribution: A study integrating metagenomic sequencing, meta-analysis and niche modeling

Fig. 3. Prevalence of pathogens associated with D. nuttalli. If there was only one study included in a certain pathogen, the positive rate would be calculated by the positive number of ticks divided by the total number of detected ticks, and without the 95% confidence interval. If there were more studies, the positive rate and 95% confidence interval would be calculated by meta-analysis.

Fig. 2 in Investigating the pathogens associated with Dermacentor nuttalli and its global distribution: A study integrating metagenomic sequencing, meta-analysis and niche modeling

Fig. 2. Study design and data sources of the meta-analysis. A comprehensive meta-analysis was performed to evaluate D. nuttalli's potential threats based on detected pathogens and geographical distribution positions. The database of D. nuttalli was constructed from four sources, including field surveys, literature review, a reference book, and an online biodiversity database (Global Biodiversity Information Facility, GBIF, https://www.gbif.org).

Fig. 1 in Investigating the pathogens associated with Dermacentor nuttalli and its global distribution: A study integrating metagenomic sequencing, meta-analysis and niche modeling

Fig. 1. Relative pathogen abundance of four D. nuttalli samples and the phylogenomic analysis of four Rickettsia genomes. (A) Pathogen abundance at the family level. (B) Pathogen abundance at the genus level. (C) The phylogenetic tree of four Rickettsia assemblies. The phylogenetic tree of four Rickettsia assemblies (Rickettsia conorii subsp. raoultii str XinjiangF1, Rickettsia conorii subsp. raoultii str XinjiangF2, Rickettsia conorii subsp. raoultii str XinjiangF3, and Rickettsia conorii subsp. raoultii str XinjiangM1) was built with 28 other publicly available established or proposed Rickettsiales species. The tree was inferred by IQ-TREE based on 277 single-copy orthologs identified by OrthoFinder. Anaplasma phagocytophilum and Ehrlichia ruminantium were two outgroup species.

Fig. 5 in Investigating the pathogens associated with Dermacentor nuttalli and its global distribution: A study integrating metagenomic sequencing, meta-analysis and niche modeling

Fig. 5. Global potential distribution of D. nuttalli. The red area indicates greater possibilities of suitability for D. nuttalli, while the blue area is less likely to be suitable for D. nuttalli.

Fig. 4 in Investigating the pathogens associated with Dermacentor nuttalli and its global distribution: A study integrating metagenomic sequencing, meta-analysis and niche modeling

Fig. 4. Geographical distribution of D. nuttalli. D. nuttalli lived mainly between 23◦–53◦ latitude and 76◦–133◦ longitude in the Northern Hemisphere. Triangles represent the locations in prefecture-level regions, while circles represent the distribution locations in county-level regions. The green circles represent points from GBIF, the yellow circles are points from literature, the purple circles represent the points from the field survey and the blue points are points from a reference book. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Figure S1 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland

Figure S1. Bayesian consensus tree of the Mesobuthus caucasicus complex reconstructed from mitochondrial DNA sequences.

Figure 9 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland

Figure 9. Phylogeny the Mesobuthus caucasicus complex reconstructed using mitochondrial DNA sequences. The Przewalski's scorpion (M. przewalskii) is deeply diverged from other species and the Chinese scorpion (M. martensii) belongs to the species complex. Node supports are shown by bootstrapping probabilities from 1000 replicates and Bayesian posterior probabilities.

Figures 1–8 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland

Figures 1–8. Mesobuthus przewalskii stat. nov., from Qiemo, Xinjiang. 1. Male, dorsal view. 2. Male, ventral view. 3. Female, dorsal view. 4. Female, ventral view. 5. Male, dentition of pedipalp chela movable finger. 6. Male, dentition of pedipalp chela fixed finger. 7. Male, ventral aspect of genital operculum and pectines. 8. Female, ventral aspect of genital operculum and pectines. Scale bars: 1–4 = 5.0 mm; 5–8 = 2.0 mm.

Figure 11 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland

Figure 11. Ecological niche models of Mesobuthus scorpions. Potential distribution areas for the Przewalski's scorpion M. przewalsii (purple) is shown together with the Chinese scorpion M. martensii (green) and other species of the M. caucasicus complex (yellow). The entire Tarim Basin and adjacent Gobi region are suitable for survival of M. przewalskii. No area to the west of the Tianshan Mountains and the Pamir Plateau is suitable for M. przewalskii, and similarly no area to the east of the Tianshan Mountains and the Pamir Plateau is suitable for other species of the M. caucasicus complex. There are overlaps in predicted suitable distribution areas between M. przewalskii and M. martensii along the northeast edge of the Qinghai-Tibet Plateau. The suitable areas in the Junggar Basin and to the north of the Tianshan Mountains are likely due to over prediction of the model, because M. przewalskii does not occur in these regions. Ecological niche model for M. martensii was adopted from Shi et al. 2007.

Figure 10 in Genetic analysis and ecological niche modeling delimit species boundary of the Przewalski's scorpion (Scorpiones: Buthidae) in arid Asian inland

Figure 10. Phylogenetic network for the Mesobuthus caucasicus species complex. Although the interrelationships between species is poorly resolved, no reticulations have occurred in the most recent common ancestors for each species. The Przewalski's scorpion M. przewalskii is clearly diverged from other member of the species complex and warrants a species rank. The divergence of the Chinese scorpion M. martensii is comparable to the divergences among the members of the species complex.