Phylogenetic scale in ecology and evolution

Aim

Many important patterns and processes vary across the phylogeny and depend on phylogenetic scale. Nonetheless, phylogenetic scale has never been formally conceptualized, and its potential remains largely unexplored. Here, we formalize the concept of phylogenetic scale, review how phylogenetic scale has been considered across multiple fields and provide practical guidelines for the use of phylogenetic scale to address a range of biological questions.

Innovation

We summarize how phylogenetic scale has been treated in macroevolution, community ecology, biogeography and macroecology, illustrating how it can inform, and possibly resolve, some of the longstanding controversies in these fields. To promote the concept empirically, we define phylogenetic grain and extent, scale dependence, scaling and the domains of phylogenetic scale. We illustrate how existing phylogenetic data and statistical tools can be used to investigate the effects of scale on a variety of well‐known patterns and processes, including diversification rates, community structure, niche conservatism or species‐abundance distributions.

Main conclusions

Explicit consideration of phylogenetic scale can provide new and more complete insight into many longstanding questions across multiple fields (macroevolution, community ecology, biogeography and macroecology). Building on the existing resources and isolated efforts across fields, future research centred on phylogenetic scale might enrich our understanding of the processes that together, but over different scales, shape the diversity of life.     

甘肃省麦积山景区——生态过渡带自然和文化遗产杰出范例

直到现在,生物多样性管护的主要注意力放在热点地区,但T．B．Smith等生态学家提出,管护战略必须把注意力不仅放在热点地区。而且也耍放在相联系的过渡带。他们争论说后者区域可能保有许多种群之间的适应变异,并因而对于生物多样性的产生和保持很重要。虽然生态过渡带常常拥有高的物种丰富度,但它们大多数是广泛分布的物种,它们的分布范围在生态过渡带相遇。甘肃省的麦积山景区是我国生态过渡带的自然和文化遗产地的杰出代表。麦积山景区不仅具有温凉、半湿润、四季分明的气候和复杂的地质地貌与土壤条件,使它的生物多样性独特丰富,具有过渡的特点,为我国同纬度其它地区无法相比,它的古文化遗存也丰富多彩,在一定程度上展现了印度佛教文化向中国化的过渡。     

齿痛消炎灵颗粒联合牙周激光对牙周炎的应用效果及对口气和舌苔指标的影响

摘要 目的：探讨齿痛消炎灵颗粒联合牙周激光对牙周炎的应用效果及对口气和舌苔指标的影响。方法：选取我院2020年7月到2023年7月收治的80例牙周炎患者,分为观察组与对照组,各40例。对照组采取常规治疗与口服齿痛消炎灵颗粒,观察组以对照组为基础,增加牙周激光治疗。对比两组患者临床疗效,对比其治疗前与治疗4周后菌斑指数（PLI）,出血指数（BI）、探诊深度（PD）、临床附着丧失（CAL）相关牙周健康指标,口气感官值（OS）、口腔挥发硫化物（VSCs）相关口气指标以及舌苔厚度（Tt）、舌苔面积（Ta）相关舌苔指标变化。结果：观察组治疗总有效率较对照组高（P＜0.05）;治疗前两组患者CAL、PD、BI、PLI水平对无差异（P＞0.05）,治疗后两组均降低,且与对照组相比,观察组较低（P＜0.05）;治疗前两组患者OS、VSCs水平对比无差异（P＞0.05）,治疗后两组均降低,且与对照组相比,观察组较低（P＜0.05）;治疗前两组患者Tt、Ta评分对比无差异（P＞0.05）,治疗后两组均降低,且观察组较对照组低（P＜0.05）。结论：齿痛消炎灵颗粒联合牙周激光治疗牙周炎效果较好,改善患者牙周健康程度,减少舌苔情况,改善口气情况。     

Hierarchical structure of the Sicilian goats revealed by Bayesian analyses of microsatellite information

Genetic structure and relationship amongst the main goat populations in Sicily (Girgentana, Derivata di Siria, Maltese and Messinese) were analysed using information from 19 microsatellite markers genotyped on 173 individuals. A posterior Bayesian approach implemented in the program STRUCTURE revealed a hierarchical structure with two clusters at the first level (Girgentana vs. Messinese, Derivata di Siria and Maltese), explaining 4.8% of variation (amova Ф_ST estimate). Seven clusters nested within these first two clusters (further differentiations of Girgentana, Derivata di Siria and Maltese), explaining 8.5% of variation (amova Ф_SC estimate). The analyses and methods applied in this study indicate their power to detect subtle population structure.     

Faunal changes and geographic crypticism indicate the occurrence of a biogeographic transition zone along the southern East Pacific Rise

Aim Deep‐sea hydrothermal vents have now been reported along all active mid‐ocean ridges and back‐arc basins, but the boundaries of biogeographic entities remain questionable owing to methodological issues. Here we examine biogeographic patterns of the vent fauna along the East Pacific Rise (EPR) and determine the relative roles of regional and local factors on the distribution of biodiversity associated with mussel beds along a poorly explored zone, the southern EPR (SEPR). Location East Pacific Rise. Methods A species list of macrobenthic invertebrates along the EPR was compiled from the literature and supplemented with data recovered during the French research cruise BIOSPEEDO carried out in 2004 along the SEPR. Biogeographic patterns were assessed by combining the identification of morphological species with a molecular barcoding approach. A multivariate regression tree (MRT) analysis was performed to identify any geographic breaks, and an empirical distribution of species richness was compared with predictions provided by a mid‐domain effect model. Macrofaunal community structure associated with mussel beds along the SEPR was analysed in relation to environmental factors using cluster and canonical redundancy analyses. Results Sequencing of the cytochrome c oxidase subunit I gene revealed the occurrence of several cryptic species complexes along the EPR, with the equator separating the southern and northern clades. Furthermore, during the BIOSPEEDO cruise at least 10 still unnamed species were collected between 7°25′ S and 21°33′ S. The shift in community structure identified by MRT analysis was located south of 17°34′ S or south of 13°59′ S, depending on the data used, suggesting that the southern part of the SEPR (17°25′–21°33′ S) constitutes a biogeographic transition zone in the vent fauna along the EPR. At a regional scale, latitude combined with the type of venting was significantly correlated with the community structure associated with mussel beds. Main conclusions Together, the molecular data, in situ observations, and the distribution of species suggest that the high diversity of vent fauna species presently observed between 17°25′ S and 21°33′ S is probably a result of the overlap of several distinct biogeographic provinces. We argue that this area thus constitutes a biogeographic vent fauna transition zone along the EPR.     

High levels of cryptic species diversity uncovered in Amazonian frogs

One of the greatest challenges for biodiversity conservation is the poor understanding of species diversity. Molecular methods have dramatically improved our ability to uncover cryptic species, but the magnitude of cryptic diversity remains unknown, particularly in diverse tropical regions such as the Amazon Basin. Uncovering cryptic diversity in amphibians is particularly pressing because amphibians are going extinct globally at an alarming rate. Here, we use an integrative analysis of two independent Amazonian frog clades, Engystomops toadlets and Hypsiboas treefrogs, to test whether species richness is underestimated and, if so, by how much. We sampled intensively in six countries with a focus in Ecuador (Engystomops: 252 individuals from 36 localities; Hypsiboas: 208 individuals from 65 localities) and combined mitochondrial DNA, nuclear DNA, morphological, and bioacoustic data to detect cryptic species. We found that in both clades, species richness was severely underestimated, with more undescribed species than described species. In Engystomops, the two currently recognized species are actually five to seven species (a 150-250% increase in species richness); in Hypsiboas, two recognized species represent six to nine species (a 200-350% increase). Our results suggest that Amazonian frog biodiversity is much more severely underestimated than previously thought.     

A review of Turkish saproxylic beetles from the European Red List

The conservation of beetles that depend on dying or dead wood (i.e. saproxylic), has received a great deal of attention in many parts of the world in recent years. Human activities such as urbanization and logging, and their results, e.g. global warming, destroy natural ecosystems and threaten unusual species such as Lucanus cervus (L. 1758), Rosalia alpina (L. 1758), Limoniscus violaceus (Müller 1821) and Osmoderma eremita (Scopoli 1763). Attempts have been made to conserve the habitats upon which these species depend. Although represented by a large number of species, saproxylic beetles in Turkey have not received much attention. Although some Turkish studies have acknowledged their value, comprehensive investigations of these species are very limited. The aim of this study is to make a list, from the literature, of the species that are endangered in Europe and found in Turkey, to highlight the importance of these species. The research includes 151 saproxylic beetle species belonging to the families Bostrichidae, Cerambycidae, Elateridae, Eucnemidae, Scarabaeidae, Euchiridae, Lucanidae and Mycetophagidae. The list of Turkish saproxylic beetles was prepared using the European Red List of Saproxylic Beetles. Information is provided about the IUCN Red List category in Europe, the locations of the species in Turkey, and their global geographic range. We gathered all data about these species from the international literature. Furthermore, we also include in the list certain species whose locations are not specified, but which inhabit Turkey. We obtained their records from some catalogs in Turkey. In addition to the list, we prepared three distribution maps for Turkey. The maps show distribution in Turkey of some species in the Endangered, Vulnerable and Near Threatened categories in the European Red List. It is expected that this study will lead to comprehensive studies on saproxylic beetles from Turkey.     

Protected areas in the world’s ecoregions: How well connected are they?

Protected areas (PAs) are the main instrument for biodiversity conservation, which has triggered the development of numerous indicators and assessments on their coverage, performance and efficiency. The connectivity of the PA networks at a global scale has however been much less explored; previous studies have either focused on particular regions of the world or have only considered some types of PAs.Here we present, and globally assess, ProtConn, an indicator of PA connectivity that (i) quantifies the percentage of a study region covered by protected connected lands, (ii) can be partitioned in several components depicting different categories of land (unprotected, protected or transboundary) through which movement between protected locations may occur, (iii) is easy to communicate, to compare with PA coverage and to use in the assessment of global targets for PA systems.We apply ProtConn to evaluate the connectivity of the PA networks in all terrestrial ecoregions of the world as of June 2016, considering a range of median dispersal distances (1–100 km) encompassing the dispersal abilities of the large majority of terrestrial vertebrates.We found that 9.3% of the world is covered by protected connected lands (average for all the world’s ecoregions) for a reference dispersal distance of 10 km, increasing up to 11.7% for the largest dispersal distance considered of 100 km. These percentages are considerably smaller than the global PA coverage of 14.7%, indicating that the spatial arrangement of PAs is only partially successful in ensuring connectivity of protected lands. The connectivity of PAs largely differed across ecoregions. Only about a third of the world’s ecoregions currently meet the Aichi Target of having 17% of the terrestrial realm covered by well-connected systems of PAs. Finally, our findings suggest that PAs with less strict management objectives (allowing the sustainable use of resources) may play a fundamental role in upholding the connectivity of the PA systems.Our analyses and indicator make it possible to identify where on the globe additional efforts are most needed in expanding or reinforcing the connectivity of PA systems, and can be also used to assess whether newly designated sites provide effective connectivity gains in the PA system by acting as corridors or stepping stones between other PAs. The results of the ProtConn indicator are available, together with a suite of other global PA indicators, in the Digital Observatory for Protected Areas of the Joint Research Centre of the European Commission.     

大针茅草原蛴螬群落特征研究

内蒙古典型草原的主体植被类型——大针茅(Stipa grandis)草原中,有蛴螬4科9种．构成大针茅草原蛴螬群落的4个科中,以鳃金龟科种类数、个体数为最多,主要种群的重要值排序为黑皱鳃金龟、东方绢金龟、马铃薯鳃金龟及弓斑常丽金龟．几种蛴螬在发生上大致呈3种类型：春季和秋季大量发生．如东方绢金龟;一年中密度波动较小,如弓斑常丽金龟;秋季大量发生,如黑皱鳃金龟和马铃薯鳃金龟．大针茅草原蛴螬群落的多样性特征在于秋季群落多样性和物种的丰度较高,而夏季相对较低．春季蛴螬群落种群丰度较高,但群落结构相对较单调．     

Diversity and distribution of reptiles in Romania

The reptile fauna of Romania comprises 23 species, out of which 12 species reach here the limit of their geographic range. We compiled and updated a national database of the reptile species occurrences from a variety of sources including our own field surveys, personal communication from specialists, museum collections and the scientific literature. The occurrence records were georeferenced and stored in a geodatabase for additional analysis of their spatial patterns. The spatial analysis revealed a biased sampling effort concentrated in various protected areas, and deficient in the vast agricultural areas of the southern part of Romania. The patterns of species richness showed a higher number of species in the warmer and drier regions, and a relatively low number of species in the rest of the country. Our database provides a starting point for further analyses, and represents a reliable tool for drafting conservation plans.