Biodiversity Analysis Research Articles

The Prediction of Plankton Diversity and Abundance in Mangrove Ecosystem

The abundance of phytoplankton and zooplankton have correlation with mangrove conditions in coastal area. The mangrove degradation give negative impact for abundance and diversity phytoplankton and zooplankton. The research aimed to analysis and construct prediction model of abundance and biodiversity of phytoplankton and zooplankton in mangrove ecosystem. The research used the transect method (to determine mangrove density), filtering method (to analyze abundance of phytoplankton and zoopankton) and statistical method (to develop estimation modeling of plankton abundance). The results showed that (1) the mangrove density between 250 trees/Ha - 1250 trees/Ha (2) the phytoplankton abundance were 10.675 Indv/L (in mangrove rarely) - 24.290 indv/ L (in mangrove high density), (3) the zooplankton abundance were 261 Indv/L (in mangrove rarely) - 2.204 indv/L (in mangrove high density) (4) The modelling analysis showed that (1) the phytoplankton abundance (y) = 0.0303 x2 - 22.059 x + 13004 and (2) the zooplankton abundance (y) = 0.0057x2 – 5.39 x + 1458.2, with x = mangrove densityKeywords: phytoplankton and zooplankton, mangrove density, abundance, estuary and lagoon

Updating of Makiling Biodiversity Information System (MakiBIS) and Analysis of Biodiversity Data

Abstract. Magcale-Macandog DB, Lapitan FRG, Laruya JM, Valerio JIF, Aguila JCD, Mesina CAL, Santos TMF, Cuevas ANT, Baylon KD, Silapan IM, Dimalobot R, Edrial JD, Larida NJA, Natuel FA, Perez MAGLD, Quinones SGL. 2021. Updating of Makiling Biodiversity Information System (MakiBIS) and Analysis of Biodiversity Data. Biodiversitas 22: 211-226. Mt. Makiling is a Philippine biodiversity hotspot listed as one of the 170 conservation priority areas established by the Philippine government. With the vast amount of ecological and biological information about the flora and fauna of Mt. Makiling, the Makiling Biodiversity Information System (MakiBIS) was developed to serve as a repository for these data. MakiBIS may serve as a prototype in the development of a national BIS that will be useful in addressing the need to set a national baseline, measurable targets, and indicators to facilitate the assessment of biodiversity status and as a basis for decision-making.The MakiBIS project started in 2011 and was last updated in 2014. In 2019, a new version of the information system was updated to take advantage of current web technologies in software development. The new MakiBIS’ (MakiBIS 2.0) frontend was written using ReactJS, while its backend functions were coded using NodeJS, and the database tables were compressed and optimized for faster queries. MakiBIS 2.0 was published online and can be accessed at www.makibis.com.The MakiBIS 2.0 database was populated with biodiversity information from published botanical and faunal survey studies conducted in Mt. Makiling. Biodiversity information includes taxonomic classification, botanical description, habitat, mode of reproduction, economic use, endemism, and conservation status. The MakiBIS database was analyzed for patterns, trends, distribution, and potential threats that will be useful towards the conservation and management of these biodiversity resources.

The biodiversity of fishes at the Islas Marías Biosphere Reserve, Mexico, as determined by baited remote underwater video

The Islas Marías Biosphere Reserve, made up of 4 islands in Pacific waters off central Mexico, supports a large diversity of marine life. However, scientific research was restricted for decades by the occupation of Isla María Madre by the Federal Penitentiary Colony of Mexico from 1905 to 2019. Aside from a list of coastal fish species published in 2011, little has been published about the fish biodiversity in the area. While the limited access to the archipelago may have acted as a de-facto marine reserve, there is evidence that fishing continued both legally for the benefit of the colony and illegally by trespassing vessels. In order to establish baseline ecological data for future conservation planning, we used baited remote underwater video (BRUV) surveys at all 4 islands during 3 expeditions to the archipelago in 2018. A total of 131 BRUV surveys representing ~150 h of footage were analyzed to create the most current compilation of species and abundance data on coastal marine fishes at Islas Marías. Ninety-nine species were identified, 3 of which were additions to the previous assessment. We found strong separation of fish communities based on both habitat and depth, and an association between hard-bottom habitats and high biodiversity of reef fishes. With the declaration of Islas Marías as a natural reserve and relocation of the prison in 2019, there is an opportunity for the reserve to become a priority area for marine conservation on the Pacific coast of Mexico. Spatial analyses of fish biodiversity at Isla María Cleofas can help develop sustainable management strategies at a time when the governmental jurisdiction of the iconic archipelago is uncertain.

Restoration of Cymodocea nodosa seagrass meadows: efficiency and ecological implications

Seagrass meadows play a key role in the provisioning of ecosystem goods and services. These systems are extremely vulnerable to multiple anthropogenic impacts. Therefore, there is an urgent need to develop new techniques to efficiently restore degraded seagrass meadows. Here we tested the efficacy and efficiency of a new technique of seagrass transplant (Cymodocea nodosa) using biodegradable containers. We investigated the effects of this transplant technique in the Adriatic Sea comparing the transplanted seagrass meadows with adjacent donor seagrass meadows and bare sediments used as control. We assessed the recovery rates and the ecological implications of this transplant on key ecosystems functions, including the biomass and detritus provision to local biological communities, and the effects on the biodiversity of the associated benthic fauna. Our results show that this restoration technique was successful, enabling the seagrass survival (approximately 30%) even in high‐energy conditions occurring in winter. The sediments hosting the transplanted seagrasses showed an increase of trophic availability and of rates of organic matter cycling. Despite this, 1 year after the transplant, the abundance and biodiversity of meiofaunal assemblages in the restored seagrasses were still lower than in donor seagrass meadows. These results indicate that the restoration process of seagrass meadows can take a long time, and that a multilevel approach (including the analysis of biodiversity and of the sedimentary processes and biogeochemical cycles) is needed to assess the success of restoration actions in these habitats.

Biodiversity and phylogenetic analyses using DNA barcoding rbcL gene of seagrass from Sekotong, West Lombok, Indonesia

Abstract. Stevanus, Pharmawati M. 2021. Biodiversity and phylogenetic analyses using DNA barcoding rbcL gene of seagrass from Sekotong, West Lombok, Indonesia. Biodiversitas 22: 50-57. West Lombok, Indonesia is one of the locations that is thought to have a quite high diversity of seagrass. Information on the diversity of seagrass species is important due to the important value of seagrass in the marine ecosystem. This research aimed to analyze biodiversity and phylogenetic of seagrass from Sekotong, West Lombok, Indonesia using DNA barcoding of rbcL gene. As many as 35 samples from seven morphologically identified species (Enhalus acoroides, Thalassia hemprichii, Cymodocea rotundata, Syringodium isoetifolium, Halodule pinifolia, Halophila ovalis, and H. minor) were taken from four Gilis (small island) in Sekotong. The DNA was amplified for the rbcL gene and sequence analyses using BLAST were conducted to determine the species. Phylogenetic analyses were carried out using three evolutionary algorithms using Neighbor-Joining, Maximum Likelihood and Bayesian analysis with 1000 bootstrap. The rbcL gene was successfully amplified from all samples with a maximum length of 552 bp. The phylogenetic analysis showed that clades were split by family and genera where six clades were formed (Enhalus acoroides, T. hemprichii, Halophila complex, H. pinifolia, S. isoetifolium, and C. rotundata) with more than 95% of bootstrap values for Neighbor-Joining and Bayesian. The p-distance values between species were 0.008-0.097 and the polymorphic site was not found within species. The rbcL sequences only confirmed five seagrass species out of seven morphologically identified species and the sequences generated from this study cannot discriminate Halophila ovalis and H. minor.

Геоинформационные исследования и картографирование растительности (дайджест по материалам конференции Интеркарто. Интергис. 1994–2020)

Proceedings of the International conference (ИнтерКарто. ИнтерГИС, Russia) devoted to geographical information systems for sustainable development of territories have been published annually since 1994. The articles discuss theoretical and methodological aspects of geoinformation support for environmental, economic and social aspects of sustainable de­velop­ment, issues of geoinformatics, cartography, remote sensing of the Earth, problems of environmental sustainability and environmental impact assessment. Over a quarter of a century, the conference proceedings got more than 125 articles related to the use of geoinformation technologies to the study and mapping of vegetation. The review of proceedings gives the concrete examples how to solve problems of vegetation mapping using GIS, it is focused on publications providing some examples of GIS appli­cation to the vegetation studies. The review is organized into thematic sections according the field of application of Geoinformatics: 1.Vegetation, 2. Dynamics, state and ecological functions of vegetation, 3. Biodiversity and its assessment, 4. Plant resources, 5. Monitoring of vegetation. The Vegetation section contains publications on vegetation studies and mapping performed for some regions of Russia — the North of the Far East, the Republic of Sakha (Yaku­tia), the Tyva Republic, Central Siberia, and others. More than half of the articles are devoted to vegetation dynamics, state and ecological functions of vegetation at different hierarchical levels. Some papers present the results of the studies based on new types of information sources (photographs) and visualization methods (animation). The use of geoinformation technologies to study biological diversity was included in the agenda of five conference sessions and later reflected in more than ten publications. They cover the development and creation of GIS, the use of geoinformation technologies for the analysis, assessment and mapping of biodiversity, for its monitoring and conservation. Quite a large number of articles are devoted to the study of forest resources. GIS technologies were used to solve problems of forest management, cartometric analysis of forested areas, determination of taxation indicators, systematization of forest conditions, etc. Examples of geoinformation versatile research for medicinal plant resources are given to assess their quality, resources and productivity in the region, to identify growing areas, including ones to be protected. Most of the published materials concerning to vegetation monitoring mainly relate to forests and forest management.

Decision-making and best practices for taxonomy-free environmental DNA metabarcoding in biomonitoring using Hill numbers.

Environmental DNA (eDNA) metabarcoding is raising expectations for biomonitoring of organisms that have hitherto been neglected. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference databases, taxonomy-free approaches are proposed for biomonitoring at the level of operational taxonomic units (OTUs). This is challenging, because OTUs cannot be annotated and directly compared against classically derived taxonomic data. The application of good stringency treatments to infer the validity of OTUs and clear understanding of the consequences of such treatments is especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect eDNA diversity estimates in the statistical framework of Hill numbers. We collected water eDNA samples at 61 sites across a 740-km2 river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared when using stringency treatments with increasing weighting of the OTU abundances. Our study demonstrated the usefulness of Hill numbers for biodiversity analyses and comparisons of eDNA data sets that strongly differ in diversity. We recommend best practice for data stringency filtering for biomonitoring using eDNA.

Saltmarsh rhizosphere fungal communities vary by sediment type and dominant plant species cover in Nova Scotia, Canada.

We surveyed Spartina saltmarsh sediment rhizosphere fungal communities at three saltmarshes and two timepoints in coastal Nova Scotia. Based on ITS2 Illumina miSeq rDNA data and multivariate analysis, neither sediment zone nor collection period correlated with fungal ASV richness, but collection site did. However, Shannon diversity indicated that sediment zone played a significant role in fungal diversity. For unweighted and weighted UniFrac distance, site was the major factor driving beta-diversity, with sediment zone and collection period having smaller roles. Sediment type and saltmarsh plant species may play important roles in structuring rhizosphere fungal assemblages, here dominated by ascomycetes. To our knowledge, our study is the first to assess fungal sediment communities in saltmarshes in Atlantic Canada using metabarcoding. It provides a biodiversity analysis of sediment fungi in a poorly studied but highly important ecosystem and points to their roles in nutrient cycling, blue carbon, coastal stability and coastal restoration. Our work will inform ongoing saltmarsh restoration in Atlantic Canada.

Incorporating time into the traditional correlational distributional modelling framework: A proof‐of‐concept using the Wood Thrush Hylocichla mustelina

Abstract Detailed spatio‐temporal information about geographic distributions of species is critical for biodiversity analyses in conservation and planning. Traditional correlative modelling approaches use species observational data in model calibration and testing in a time‐averaged framework. This method averages environmental values through time to yield a single environmental value for each location. Although valuable for exploring distributions of species at a broad level, this averaging is one of myriad factors impacting model quality and reliability. We sought to optimize traditional correlative niche model performance in distributional ecology contexts by incorporating time specificity into the existing modelling framework. We modified the existing framework to account for temporal dynamics in species' distributions to produce more robust, temporally explicit models. Using the Wood Thrush Hylostichla mustelina as our study species, we introduce a method of (a) deriving a temporally explicit pseudo‐absence dataset using kernel density estimates to replicate relative sampling of sites through time, and (b) incorporating temporally explicit covariates in model calibration. By accounting for location, and month and year of primary data collection, the time‐specific models successfully yielded dynamic predictions reflecting known distributional shifts in Hylocichla mustelina's annual movement pattern. The modified data preparation steps that we present incorporate temporal dimensions into traditional correlational modelling approaches improving predictive capacity and overall utility of these models for highly mobile, short‐lived or behaviourally complex species. With the ability to estimate species' niches in greater detail, time‐specific models will be able to address specific concerns of species‐level management and policy development for highly mobile and/or migratory species, as well as disease vectors of public health interest.

Relationship of taxonomic error to frequency of observation.

Biological nomenclature is the entry point to a wealth of information related to or associated with living entities. When applied accurately and consistently, communication between and among researchers and investigators is enhanced, leading to advancements in understanding and progress in research programs. Based on freshwater benthic macroinvertebrate taxonomic identifications, inter-laboratory comparisons of >900 samples taken from rivers, streams, and lakes across the U.S., including the Great Lakes, provided data on taxon-specific error rates. Using the error rates in combination with frequency of observation (FREQ; as a surrogate for rarity), six uncertainty/frequency classes (UFC) are proposed for approximately 1,000 taxa. The UFC, error rates, FREQ each are potentially useful for additional analyses related to interpreting biological assessment results and/or stressor response relationships, as weighting factors for various aspects of ecological condition or biodiversity analyses and helping set direction for taxonomic research and refining identification tools.

Assessing the ichthyofaunal diversity and trophic level from trawl bycatch of Chennai Fishing Harbour, Southeast Coast of India

The present study aimed to document the temporal diversity and trophic level of ichthyofauna from the Chennai Fishing Harbour, Southeast coast of India. The trawl bycatch consists of 45,527 ichthyofauna individuals collected fortnightly during the period June 2018 to April 2019. The recorded ichthyofaunal diversity includes 156 species belonging to 2 classes, 14 orders, 66 families, and 119 genera. The order Perciformes dominantes with 74 species (47%) followed by Scorpaeniformes (12%; 19 species) and Tetraodontiformes (11%; 18 species). Temporal diversity analysis revealed that the maximum species diversity was observed during the North-east monsoon (123 species) while the minimum was observed during the post-monsoon (107 species) period. Numerically dominant bycatch species were found to be Leiognathus equulus (6%), Equulites lineolatus (5%), Gazza achlamys (5%), Karalla dussumieri, (4%) Otolithes ruber (3%) and Nibea maculata (2%). Biodiversity analysis revealed that the Shannon–Wiener​ species diversity index ranged from 5.37 (South-west monsoon) to 5.53 (North-east monsoon) whereas the species evenness was observed from 0.77 (South-west monsoon) to 0.81 (Post-monsoon). The habitat-wise diversity analysis revealed that demersal species group was dominant (72 species; 46%) followed by reef-associated (70 species; 45%), benthopelagic (8 species; 5%), pelagic (5 species; 3%) and bathy-demersal (1 species; 1%). The results of the trophic level shows that the bycatch fish species was dominated by top-level carnivores (49%) followed by mid-level carnivores (26%), apex predator (19%), primary carnivores (5%) and herbivores or planktivores (1%). The IUCN categories of bycatch species are mostly classified as Not Evaluated, Least Concern, Data Deficient and Vulnerable viz., 58%, 36%, 5% and 1% respectively. The present study also gives information on juvenile fish that are encountered in trawl bycatch along the Chennai coast. The outcome of the study gives baseline information on the bycatch diversity which paves the way for the sustainable exploitation and also the management of exploited fisheries resources in this region.

On the relative importance of landscape variables to plant diversity and phylogenetic community structure on uninhabited islands, South Korea

Although there have been methodological advances in the analysis of biodiversity and landscape properties, most studies in landscape ecology primarily explore whether certain landscape properties, such as island area and isolation, have universal effects on species-centric measures. We assessed how landscape variables drive species richness, phylogenetic diversity (PD), and phylogenetic community structure. Moreover, we explored the dominant processes structuring plant community assembly, including phylogenetic community structure. We used plant data from 235 uninhabited islands in the western and southern seas, South Korea. Species richness, Faith’s PD, and standardized effect size of mean pairwise phylogenetic distance (SES.MPD) were quantified for three plant groups, all, woody, and herbaceous plants for each island. Island area, distance from mainland, habitat heterogeneity, and structural connectivity were also calculated to examine the relationships between indices of plant diversity and community structure. The relative importance of landscape variables differed among indices of diversity and community structure as well as among plant groups. Island area and distance from mainland were the main drivers of species richness and PD across plant groups, whereas distance from mainland significantly affected community structure measured by SES.MPD. We found that the community structure in islands farther from mainland showed phylogenetic clustering patterns driven by niche-based deterministic processes across the three plant groups. We found that community structure analysis provides more information related to ecological processes and assembly mechanisms than diversity indices alone. Therefore, we recommend that community structure analysis with plant diversity should be implemented as an additional measure of biodiversity for landscape ecology and for conservation planning in island ecosystems.

Prokaryotic communities of technozems of the spoil heaps of Kursk magnetic anomaly

Background. Spoil heaps chronosequences are convenient models to analyze the succession of microbiome during restoration of anthropogenically disturbed landscapes. The investigation of the heavy metal content in lands with mining activity, can be used as an indicator of ecosystem recovery.
 Materials and methods. Objects were technozems of 1-year, 25- and 50-year-old embryonic soils, and control soil under forest. Quantitative polymerase chain reaction (qPCR) and NGS-sequencing of V4 region of 16S rRNA gene were applied. Results. During the soil-forming process, an increase organic carbon and nitrogen, as well as a gradual increase archaeal 16S rRNA gene copies and in the number of Bradyrhizobiaceae, Blastocatellaceae, Xantobacteriaceae. Although we found a number of taxa that increased during soil-forming process (Thaumarchaeota, Bradyrhizobiaceae, Blastocatellaceae, Xantobacteriaceae), technozems of different ages had a similar structure and diversity of prokaryotic communities, differing from a nature soil. Biodiversity analysis revealed that technozems generally had a similar structure and diversity of prokaryotic communities, significantly differing from the mature soil a specific clusterization of microbiomes. The HM contents and bacterial abundances remained at the same level in chronosequence.
 Conclusions. The 50 years of soil development on overburden spoil heaps is not enough for the recovery from HM contamination and restoration of soil ecosystem functioning.

Structure of the Botanical Diversity of the Utrish–Tuapse Variant of the Crimean-Novorossiysk Orobiom

A regional assessment of the Crimean-Novorossiysk orobiome, which is considered a reference unit for the inventory and analysis of mountainous biodiversity, is based on the concept of ecosystem diversity. The altitudinal zonal structure of the vegetation cover is studied on the example of the Utrish–Tuapse geographic variant of the orobiome associated with the northwestern Caucasus, in accordance with which the spatial differentiation of flora and plant communities is formed. A quantitative substantiation of the biota and abiotic parameters characterizing the botanical and geographical uniqueness of the orobiome is given. The spectrum of altitudinal zonality of vegetation is determined, a quantitative assessment of floristic diversity by zones is given, and some features of the spatial structure of the diversity of communities in the mountainous area are shown.

No one-size-fits-all solution to clean GBIF.

Species occurrence records provide the basis for many biodiversity studies. They derive from georeferenced specimens deposited in natural history collections and visual observations, such as those obtained through various mobile applications. Given the rapid increase in availability of such data, the control of quality and accuracy constitutes a particular concern. Automatic filtering is a scalable and reproducible means to identify potentially problematic records and tailor datasets from public databases such as the Global Biodiversity Information Facility (GBIF; http://www.gbif.org), for biodiversity analyses. However, it is unclear how much data may be lost by filtering, whether the same filters should be applied across all taxonomic groups, and what the effect of filtering is on common downstream analyses. Here, we evaluate the effect of 13 recently proposed filters on the inference of species richness patterns and automated conservation assessments for 18 Neotropical taxa, including terrestrial and marine animals, fungi, and plants downloaded from GBIF. We find that a total of 44.3% of the records are potentially problematic, with large variation across taxonomic groups (25–90%). A small fraction of records was identified as erroneous in the strict sense (4.2%), and a much larger proportion as unfit for most downstream analyses (41.7%). Filters of duplicated information, collection year, and basis of record, as well as coordinates in urban areas, or for terrestrial taxa in the sea or marine taxa on land, have the greatest effect. Automated filtering can help in identifying problematic records, but requires customization of which tests and thresholds should be applied to the taxonomic group and geographic area under focus. Our results stress the importance of thorough recording and exploration of the meta-data associated with species records for biodiversity research.

Land system diversity, scaling laws and polygons map analysis

AbstractNumerous lines of evidence have been presented in the literature that show the patterns of pedodiversity and biodiversity are very similar. One of the most corroborated patterns lies in the fits of the relationships between biodiversity and soil diversity to power laws according to the increase in study area. Several authors have analysed the presence of fractal and multifractal features in pedodiversity and biodiversity analyses. Similarly, it has also been found that valuable information can be extracted from the polygons of soil and vegetation maps, which also have surprising similarities. These approaches concern information on the spatial distribution of natural resources. However, other more artificial but interesting maps and their comparison have been neglected by such studies. Land systems maps and their georeferenced databases fall into this latter category, and they include most of the soil‐forming factors. In this paper a georeferenced land system database and map were analysed and the results compared with those obtained in previous pedodiversity and biodiversity studies, primarily the spatial patterns of the polygons. The results showed that the analysed land system map units followed the same patterns that were previously found in pedodiversity and biodiversity studies; that is, the power law concerning richness–area relationships. The same patterns occur with the number of polygons. Some geographers claim there is a “law” that states that there are far more small things/objects than larger ones across several orders of magnitude in geographic space and thus this regularity conforms to scaling laws, independent of the resource involved. The results obtained corroborate this conjecture irrespective of whether natural resources or artificial cartographies were analysed. This paper represents a first test of land use maps; additional work in this area is needed.Highlights Spatial patterns detected in natural and land system maps seem to be similar Composite GIS maps have the same spatial patterns as their base maps. Soil and land system units conform to long‐tail or heavy tail distributions. Soil maps and land system maps conform to power laws, fingerprints of fractal structures There are more small polygons than large ones across several magnitude orders on choropleth maps.

Diversity of zooplankton along the northern part of Vembanad lake, Kerala, India

Zooplankton samples collected from six stations, along the Kollam Kottappuram waterway (National Waterway 3) on the northern part of Lake Vembanad on monthly intervals during October 2018 to September 2019 formed the basis of this study. The samples were analysed both qualitatively and quantitatively by adopting standard methods. 23 groups of zooplankton were recorded from the study area. Out of these, a maximum of 18 groups were recorded from station 1 (Cochin bar mouth) and a minimum of 9 groups from station 6 (Kottappuram). Overall average density of zooplankton in the study area was 3044 numbers per 100 m3 . Station-wise studies indicated that the average zooplankton density was maximum (4882 per 100 m3 ) at station 2 (Kadamakudy) and minimum (1649 per 100 m3 ) at station 5 (Azhikode bar mouth). Among the different groups of zooplankton in the study area, a maximum of 79% was contributed by copepods, 14% by rotifers while the remaining groups contributed less than 2% each. Month-wise analysis indicated the maximum density during September and the minimum during January. Biodiversity analyses were carried out by Primer v. 6 software. From the cluster analysis and Bray-Curtis similarity matrix, July and August months showed the maximum similarity of species composition compared to all other months.

Noise does not equal bias in assessing the evolutionary history of the angiosperm flora of China: A response to Qian (2019)

AbstractIn response to our paper on the evolutionary history of the Chinese flora, Qian suggests that certain features of the divergence time estimation employed might have led to biased conclusions in Lu et al (2018). Here, we consider Qian's specific criticisms, explore the extent of uncertainty in the data and demonstrate that (i) no systematic bias toward dates that are too young or too old is detected in Lu et al.; (ii) constraint of the crown age of angiosperms does not bias the generic ages estimated by Lu et al.; and (iii) ages derived from the Chinese regional phylogeny do not bias the conclusions reported by Lu et al. All these analyses confirm that the conclusions reported previously are robust. We argue that, like many large‐scale biodiversity analyses, sources of noise in divergence time estimation are to be expected, but these should not be confused with bias.

Exploring the scaling law of geographical space: Gaussian versus Paretian thinking

AbstractA debate has occurred concerning the laws of scale and the fractal nature of geographical space. Biodiversity and pedodiversity studies show the emergence of fractal structures such as taxa‐area relationships. Biodiversity and pedodiversity are natural resources, although some consider pedotaxa to be artificial. The studies carried out to date emphasize that many pedodiversity and biodiversity spatial patterns converge at the same regularities. Many of these studies used natural resources maps and their digital databases. Information is extracted from the taxa types contained in each polygon and the areas covered. However, the structure of the maps (number, area, fragmentation, etc.) has rarely been a matter of study. When map structure was studied, intriguing similarities were observed in pedodiversity and biodiversity analyses. To understand whether these similarities also appear in other types of spatial entities that are more artificial, a review of geospatial analyses that studied topics such as urban maps, land system maps, etc., was undertaken. The main variables in these maps are manmade and/or combinations of natural resources data layers. Regularities detected in the geospatial information of these latter topics also seem to conform to results obtained when analysing natural resources maps such as soils, rock types, landforms, plant communities, etc. Thus, some geographers consider the idea that there are far more small things/objects than larger ones across several orders of magnitude in geographic space to be a law. Some geographers also contend that the classical “Gaussian thinking” and its statistical tools should be replaced by a “Paretian thinking” and its related statistical tools. This paper analyses the above topics as well as the lack of adequate data and types of cognitive maps we use in our modern scientific society, supporting the conjecture that that we should include Paretian thinking in our research at least in the same way we use Gaussian thinking.Highlights Long tail distributions, power laws and fractal‐like structures are ubiquitous in geospatial analysis. Scale invariance of natural and artificial map structures seem to be the rule. The Paretian approach appears to be more appropriate than the Gaussian approach for many purposes. Our cognitive maps and brain processing follow Paretian thinking in many instances.

The Pull of the Recent revisited: negligible species-level effect in a regional marine fossil record

AbstractQuantifying true patterns of biodiversity change over the Cenozoic has major implications for all of biology and paleontology but is still a source of significant debate. The problem centers on the magnitude and nature of several well-known sampling effects and analytical biases in the fossil record, including the Pull of the Recent. We test the effect of the Pull of the Recent at both generic and species levels on the exemplary New Zealand Cenozoic marine mollusk fossil record. We examine several biological traits of species to determine whether particular attributes of taxa control their likely presence or absence in the youngest fossil record (<2.4 Ma). We demonstrate that, for a tectonically active region, the Pull of the Recent does not exert a strong effect on apparent diversity patterns of genera and species over the Cenozoic at temporal scales typically used in global and regional biodiversity analyses. This result agrees with previous studies quantifying the effect of the Pull of the Recent in the marine and terrestrial realms at the genus level. The effect of the Pull of the Recent, although small, is greatest for the youngest fossil record (<2.4 Ma), particularly for species. This increase cannot easily be explained by effects related to shell mineralogical composition, size, habitat, taxonomic class, or lithification. The small effect that the Pull of the Recent exerts on the New Zealand molluscan fossil record implies that the apparent rise in regional marine diversity during the Cenozoic represents a true biological signal and/or reflects other confounding effects not considered here.