Philippa Kaur

Genotyping control and datasets creationsAfter filtering the initial raw dataset of 1,071 goats for poor quality genotype and related animals we obtained the dataset used for the haplotype sharing analysis, which included 980 animals and 48,396 SNPs. This dataset was further pruned for linkage disequilibrium (LD; r2  More

MDE hypothesisGradient features of species diversity of plant communities refer to regular changes in species diversity along a gradient of environmental factors at the community level12,43. The altitudinal gradient includes gradient effects of multiple environmental factors. It is therefore important to study altitudinal patterns of species diversity to reveal changes in biodiversity along environmental gradients. The width and range of species distribution along geographical gradients reflect the ecological adaptability, diffusivity, and evolutionary history of species44. To some extent, geographical distribution patterns of species diversity can be interpreted as outcomes of synthetic actions across altitudinal gradients resulting from eurychoric species with a greater distribution width and stenochoric species with a smaller distribution range along geographical gradients44. Hence, the MDE, environmental gradient, distribution area, human disturbance, and habitat heterogeneity all have effects on the vertical distribution patterns of species diversity45,46. According to the MDE hypothesis, there is overlap in the distribution range of species along altitudinal gradients; the highest overlap intensity occurs at intermediate elevations. There is relatively low overlap intensity at low and high elevation areas, and the peak values of species diversity occur at intermediate elevations.In this study, forest ecosystems on the Loess Plateau were separated into three communities: tree, shrub, and herb communities. The altitudinal patterns and factors that influence species diversity of mountainous vegetation were then determined at the plant community level related to the form and family of the plant species. We discovered that the family numbers of the herb, shrub, and tree communities reached their greatest values at intermediate, intermediate, and lower elevations, respectively. We also discovered that correlations of species diversity indices with elevations conformed to unimodal change patterns for herb, shrub, and tree communities, which presented their greatest values at higher, lower, and intermediate elevations, respectively. This showed that MDE is another important factor that affects the distribution patterns of species diversity along regional altitudinal gradients, in addition to temperature, precipitation, and the terrain.A large number of studies have already verified that MDE is a significant mechanism that influences the gradient patterns of species diversity. MDE not only functions along altitudinal gradients but also acts along latitudinal and temporal gradients28,29,30,47. However, the effects of MDE on species diversity patterns are highly controversial. Some studies considered MDE to be the main factor that results in unimodal patterns of species diversity47,48, whereas other studies affirmed that the effects of MDE are smaller in contrast to the functions of the distribution area, environmental gradient, and other factors29,30. Besides MDE, other factors may also lead to unimodal vertical gradient patterns of species diversity, such as plant productivity, human disturbance, and the regional climate45,49. Our research indicated that the relationships of species diversity conformed to unimodal change patterns along various elevations for mountainous herb, shrub, and tree communities in a semi-arid region of the temperate zone. It can be concluded that vertical patterns of species diversity with a unimodal type may be a more universal phenomenon, relative to monotonic decreasing or increasing patterns of species diversity with increasing elevations.Factors influencing MDE at the plant community levelIn this study, more forbs and grasses were found at higher elevations, whereas more sedges occurred at lower elevations. The responses of the importance values of tree species to the altitudinal gradient demonstrated the following variation patterns: evergreen coniferous trees had higher importance values than deciduous coniferous trees, followed by deciduous broad-leaved trees. This showed that MDE was influenced by species life form. The species diversity of different life forms responded differently to the environment, and plant species with different life forms presented different diversity patterns along altitudinal gradients50. In New Zealand, the number of mountainous plants species decreased with increasing elevations and the total species number of all plants also decreased significantly, while species diversity had no significant distribution trend in response to elevation when plants with different life forms were considered under different layers of plant communities51.MDE is a common pattern of species diversity of mountainous plants with changing elevations. Our study area, located on the Loess Plateau of China, belongs to a semi-arid mountainous region in the temperate zone where the maximum species diversity of the tree community occurred at intermediate elevations. This finding was in accordance with the MDE hypothesis. Research from the Kinabalu Mountains in Sabah, Malaysia, indicated an obvious MDE pattern of species number linked to elevations52. On the Haleakala Mountains, Hawaii, USA, the highest species diversity occurred at intermediate elevations, which was also in accordance with the MDE hypothesis53. The MDE hypothesis was also proved by studies conducted in the Yu Mountains of Taiwan and the Emei Mountains of Szechwan in China54. However, the MDE pattern of species diversity in tree communities is caused by precipitation, which is the highest at intermediate elevations52. This situation also occurred in the herb community.There are many factors that affect the distribution of herbaceous plants, so the variations in species diversity in the herb community with elevations are complex55. In this study, we found that the herb community exhibited higher species diversity at higher elevations; more forbs and grasses were distributed at higher elevations, whereas more sedges were distributed at lower elevations. In the Siskiyou Mountains in Oregon, USA, the species diversity of herbaceous plants had a significantly positive correlation with elevation. This correlation occurred mainly due to an increase in the number of grass species, which was the primary reason that radiation was enhanced by a drastic reduction in community coverage as a result of increasing elevations. Consequently, there was an increase in the species diversity of herbaceous plants24. A decrease in species diversity with increasing elevations is a more familiar pattern for herbaceous plants in temperate56 and tropical22 forests.We also discovered that the family numbers of herb and shrub species all showed unimodal change patterns with high values at their central elevations in this semi-arid region. This conformed to the MDE hypothesis as well. In arid temperate grasslands, species diversity indicated an MDE distribution pattern. For example, the species diversity of herbaceous plants presented an MDE pattern in drought areas of the Siskiyou Mountains57. However, in semi-humid mountains in the temperate zone, the species diversity of herbaceous plants was principally in control of the community structure, and community coverage did not respond uniformly to elevation. Studies in New Zealand showed that there were no evident distribution trends for species diversity of herbaceous plants along elevations51. In low bush communities of Chile, the species diversity of herbaceous plants declined with increasing elevations after longstanding succession, but it increased during the early stage of succession58. Therefore, relationships between the species diversity of herb species and elevations were not completely clear in semi-humid regions.The major factors that control the distribution areas of species differ among different families and genera, and thus the vertical distribution patterns of species diversity differ22. We concluded that the family number of the tree species had a maximum distribution at lower elevations, unlike herb and shrub species; meanwhile, the responses of the importance values to the altitudinal gradient in the tree community were also different among evergreen coniferous trees, deciduous coniferous trees, and deciduous broad-leaved trees. These differences may have been related to environmental factors. Due to various distribution patterns of environmental parameters with elevations, the distribution patterns of species diversity showed large changes along elevations59. For example, the distribution of fern and Melastomataceae species is principally related to humidity, that of Acanthaceae and Bromeliaceae species is correlated with temperature, and that of Araceae species is related to transpiration59. Research conducted in the Gongga Mountains, China, showed that the species diversity with different floral components exhibited different distribution patterns along elevations due to differences in the environment and species origin60. We also discovered that the importance values of dominant families in the shrub (Rosaceae) and tree (Pinaceae) communities exhibited changing patterns in contrast to MDE. In our study, only the family numbers in the herb and shrub communities, as well as species diversity in the tree community, conformed to the MDE hypothesis. Therefore, we concluded that the MDE hypothesis of species diversity of mountainous vegetation is influenced by the species life form and family of different plant communities in the temperate semi-arid region of China.Factors influencing plant species diversity at the environment levelThe altitudinal distribution patterns of the plant community diversity had greater discrepancies in mountainous regions and between different community types, which might be connected to regional environmental conditions, relative heights of mountains, and the geological landscape35. Concerning the altitudes of mountains, serious human disturbances (e.g., deforestation, grazing, and land-use conversion) had negative effects on biodiversity in low-altitude regions61. In high-altitude regions, the cold climate slowed down plant growth and soil development, while other harsh environments exceeded the tolerance limits for growth of the majority of species, such as by intense solar radiation or large temperature differences between day and night62. In the middle-altitude regions, the species diversity was relatively higher due to less human disturbances and the formation of transition zones of plant species differentiation between the low- and high-altitude regions62. Hence, the plant community diversity and its altitudinal gradient patterns in mountainous regions were largely influenced by regional climate and human disturbances.Comparisons of the diversity at different levels indicated that the responses of the plant community diversity to the environment were not the same for diverse gradations, and different species exhibited different gradient patterns owing to restrictions from environmental factors63,64. The primary factors leading to the altitudinal differentiation of diversity included the temperature, moisture, soil nutrients, and succession process65. In our study area, compared with Guancen Mountain and Guandi Mountain, Wulu Mountain at the lower latitude of the Lvliang Mountains had a lower altitude and was located in the continental monsoon subhumid climate region of the warm temperate zone, making it suitable for the growth of secondary forests and shrub vegetation. However, the vegetation growth in the herb layer was restricted in Wulu Mountain, making diversity in the herb layer the greatest on Guandi Mountain at the middle latitude of the Lvliang Mountains35. This showed that the plant species diversity in the east of the Loess Plateau changed with the altitude, while being affected by complicated habitat conditions such as latitude and human disturbances. This characterization of the study area was correlated with the unimodal patterns observed. In this study, we observed that the family numbers of the herb and shrub communities presented unimodal patterns across an altitudinal gradient; the importance values of dominant families also presented unimodal patterns in the shrub and tree communities; and the species diversity indices of the herb, shrub, and tree communities conformed to unimodal change patterns following an altitudinal gradient as well.In our recent studies on the species diversity of herbaceous communities in the Lvliang Mountains66, we found that the results calculated for β-diversity using different indices revealed the highest value for the Cody index and the lowest value for the Bray–Curtis index at altitudes between 1900 and 2000 m, indicating that areas located between 1900 and 2000 m form a transition zone in which the herbaceous community undergoes a rapid process of species renewal and changes in its composition. The results for γ-diversity indicated a pattern of unimodal variation in relation to altitude. Changes in altitude gradient had highly significant impacts on changes in temperature and humidity, indicating that various environmental factors (notably humidity and temperature) and human disturbances had combined effects on changes in the values of the α-diversity indices.At present, it is widely believed that the formation of herbs in different life forms was principally impacted by precipitation, whereas in areas with similar rainfall, water, heat, and light conditions need to be considered. These conditions chiefly included average annual precipitation, accumulated temperature, and illumination time67. In this research, we observed that herb and tree species in different life forms showed different trends with altitudinal gradients in the Lvliang Mountains. At higher elevations, forbs and grasses grew well, whereas sedges grew well at lower elevations. The responses of different tree life forms to the altitudinal gradient were greater for evergreen coniferous tree species than for deciduous coniferous tree species and deciduous broad-leaved tree species. From the north to the south in the Lvliang Mountains, increases in the average annual precipitation increased the number of species and components of the annual herbs, while the hydrothermal matching requirements of Guandi Mountain at the middle latitude were preferred for annual herb growth in comparison with Guancen Mountain at the higher latitude67. However, considering whole mountains, the Lvliang Mountains located in the continental monsoon climate region of the warm temperate zone had four distinctive seasons with drought and wind in the spring, and a quick rise in air temperatures, and larger diurnal temperature differences35. These conditions conformed to the habitat features of herbs and trees. Hence, the hydrothermal distribution status affected by latitude and human disturbances determined the altitudinal distribution patterns of plant community diversity in the Lvliang Mountains.The MDE at different elevationsIn this study, we discussed the MDE of mountainous vegetation on the Loess Plateau with an elevational range from 1324 to 2745 m, including tree, shrub and herb community. This range was a very large elevation range for a case study, but a very short range in comparison to global elevation ranges, which extended from the sea level to well over 8000 m (though the highest locations did not have any vegetation). Therefore, owing to this limitation, the results we obtained in this research were suitable for lower elevation mountains in semi-arid areas.The MDE was changed with different elevations and vegetation layers. In studies on the Daiyun Mountains with an elevation from 900 to 1600 m, the phylogenetic diversity and species diversity of tree community indicated an intermediate high expansion pattern along elevations and their peak values all appeared at the elevation of 1200 m68. This conclusion conformed to the MDE pattern. In our studies on the Lvliang Mountains with an elevation from 1459 to 2610 m, higher species diversity of tree community was observed at intermediate elevations with a peak value being at the 2000 m, which conformed to the MDE pattern either. Therefore, at smaller elevations less than 2600 m, species diversity of tree conformed to the MDE pattern.When an elevation reached 2700 m on the Lvliang Mountains, the vegetation types changed to shrub and grass, and only their family numbers followed the MDE pattern across an altitudinal gradient. Slimily, the species richness of shrub and herb layer showed an obvious “lateral pattern” on an elevational gradient from 2950 to 3750 m on the Three River Headwater, both reaching the maximum value at the 3150 m; while with the rise of altitude, α diversity of shrub layer and herb layer showed a “wave”-shaped changed trend, reaching the lowest value at the 3550 m69. It illustrated that species diversity of shrub and grass did not conform to the MDE pattern completely at medium elevations from 2700 to 3700 m.As for an elevation extending from 3000 to 4400 m on the Gongga Mountains, the vegetation type was alpine meadow, and the species richness index presented an obvious unimodal pattern with a peak value at the 3850 m, which accorded with the MDE pattern70. Similarly, studies on an alpine meadow on the Gannan revealed that the number of richness, Shannon-Weiner index and phylogenetic diversity of plant community all showed a “humped-back” relationship with the increase of altitude from 3000 to 4000 m, and reached the maximum value at the 3800 m71,72. Thereby, at greater elevations more than 3800 m, species diversity of alpine meadow conformed to the MDE pattern.However, when an elevation exceeded 5000 m, research object on species diversity were not vegetation but animals along an altitudinal gradient. For example, on the Himalaya Mountains with an elevation from 3755 to 5016 m, the ant species richness illustrated a “unimodal curve” pattern along the rise of altitude, and the Shannon–Wiener index and Fisher α index of ant community commonly expressed the “Multi-Domain Effect” phenomenon73. Another research on mammalian richness was also conducted on the Himalaya Mountains. It concluded that most of elevational species richness patterns were hump-shaped from 100 to 6000 m on the Himalayas Mountains74. As a result, the MDE pattern was also extremely common in animal communities. More

The catenary sequence of soilsThe catena of Andosols down a slope near a hot spring in the Valley of Geysers was subdivided into four thermal zones (Fig. 1a–e), which are described below.Figure 1Location of study area (a–c), soil pits along the catena (d, e) and photos of soil pits (f–i). (a b) Study area location. Soil map is from133 (open access) with additions and corrections by I.N. Semenkov based on the map of soil temperature at a depth of 15 cm in the Valley of Geysers131 and the soil names from44 using CorelDraw X7 software (https://www.coreldraw.com/). (c) Top view of the left side of the Geysernaya River with the body of a catastrophic landslide, a visitor center (in the left lower part) and the location of the transect studied (1–15). (d) The location of transect studied. (e) A schematic profile of the catena studied with numbered soil pits. The main soil pits selected for comprehensive analyses (see section ‘Soil analyses’) are in red. (f) Non-heated Eutrosilic Silandic Andosols (Arenic, Cutanic) on pyroclastic material (pit no 16, Zone I), within levelled parts of the interfluve, under tall-herb meadow communities with local patches of Erman’s birch woods. (g) Slightly heated Eutrosilic Aluandic Andosols (Cutanic, Loamic, Natric) in the upper part of the catena, on hydrothermally altered sandy-loamy pyroclastic material (pit no 12, Zone II), on slightly heated slopes, under tall-herb meadows. (h) Moderately heated Eutrosilic Gleyic Aluandic Andosols (Loamic, Reductic, Protosalic, Hyperthionic) in the middle part of the catena, on hydrothermally altered clayey pyroclastic material (pit no 9.1, Zone III), under different moss and ‘microzonal’ communities. (i) Hot Gleyic Aluandic Andosols (Clayic, Reductic, Salic, Hyperthionic) in the lower part of the catena, on hydrothermal clays (pit no 4, Zone IV), on most heated bare slopes.Full size imageZone I. Non-heated Eutrosilic Silandic Andosols (Arenic, Cutanic) under Kamchatka’s tall herb communities and fragmented Erman’s birch woodsNon-heated Andosols with temperatures of 50 with very small amounts of PM5–50 ( More

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