Estimates Of Species Diversity Research Articles

Comparing Morphological and Molecular Estimates of Species Diversity in the Freshwater Genus Synura (Stramenopiles): A Model for Understanding Diversity of Eukaryotic Microorganisms.

We performed a comparison of molecular and morphological diversity in a freshwater colonial genus Synura (Chrysophyceae, Stramenopiles), using the island of Newfoundland (Canada) as a case study. We examined the morphological species diversity in collections from 79 localities, and compared these findings to diversity based on molecular characters for 150 strains isolated from the same sites. Of 27 species or species-level lineages identified, only one third was recorded by both molecular and morphological techniques, showing both approaches are complementary in estimating species diversity within this genus. Eight taxa, each representing young evolutionary lineages, were recovered only by sequencing of isolated colonies, whereas ten species were recovered only microscopically. Our complex investigation, involving both morphological and molecular examinations, indicates that our knowledge of Synura diversity is still poor, limited only to a few well-studied areas. We revealed considerable cryptic diversity within the core S.petersenii and S.leptorrhabda lineages. We further resolved the phylogenetic position of two previously described taxa, S.kristiansenii and S.petersenii f. praefracta, propose species-level status for S.petersenii f. praefracta, and describe three new species, S.vinlandica, S.fluviatilis, and S.cornuta. Our findings add to the growing body of literature detailing distribution patterns observed in the genus, ranging from cosmopolitan species, to highly restricted taxa, to species such as S.hibernica found along coastal regions on multiple continents. Finally, our study illustrates the usefulness of combining detailed morphological information with gene sequence data to examine species diversity within chrysophyte algae.

High-throughput sequencing analysis reveals dynamic seasonal succession of diatom assemblages in a temperate tidal flat

Benthic diatoms are a major phytoplankton group, and play pivotal roles in coastal biogeochemical cycles and food webs. However, their community structure and diversity remain poorly understood. We investigated the variability in their taxonomic composition and diversity over 5 years in a temperate tidal flat based on high-throughput sequencing of the rbcL gene. Chao1 and Shannon species richness and diversity estimates in this study ranged from 412 to 9582 and from 2.7 to 6.3, respectively, showing higher diversity than previous estimates based on traditional morphological analyses. At the genus level, Navicula, Nitzschia, and Amphora were dominant in all seasons. However, at the 98% identity operational taxonomic unit level, seasonal changes in community structure were remarkable. A number of taxa were found only during a specific season, and only a small portion of taxa were commonly found in all seasons. This seasonal succession was mainly influenced by sediment temperatures and sand ratios. Our research provides a solid basis for the high diversity of tidal flat diatoms.

Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema species complex (Serpentes: Elapidae)

New world coralsnakes of the genus Micrurus are a diverse radiation of highly venomous and brightly colored snakes that range from North Carolina to Argentina. Species in this group have played central roles in developing and testing hypotheses about the evolution of mimicry and aposematism. Despite their diversity and prominence as model systems, surprisingly little is known about species boundaries and phylogenetic relationships within Micrurus, which has substantially hindered meaningful analyses of their evolutionary history. Here we use mitochondrial genes together with thousands of nuclear genomic loci obtained via ddRADseq to study the phylogenetic relationships and population genomics of a subclade of the genus Micrurus: The M. diastema species complex. Our results indicate that prior species and species-group inferences based on morphology and color pattern have grossly misguided taxonomy, and that the M. diastema complex is not monophyletic. Based on our analyses of molecular data, we infer the phylogenetic relationships among species and populations, and provide a revised taxonomy for the group. Two non-sister species-complexes with similar color patterns are recognized, the M. distans and the M. diastema complexes, the first being basal to the monadal Micrurus and the second encompassing most North American monadal taxa. We examined all 13 species, and their respective subspecies, for a total of 24 recognized taxa in the M. diastema species complex. Our analyses suggest a reduction to 10 species, with no subspecific designations warranted, to be a more likely estimate of species diversity, namely, M. apiatus, M. browni, M. diastema, M. distans, M. ephippifer, M. fulvius, M. michoacanensis, M. oliveri, M. tener, and one undescribed species.

A new redescription of Richtersius coronifer, supported by transcriptome, provides resources for describing concealed species diversity within the monotypic genus Richtersius (Eutardigrada)

Richtersius coronifer, the nominal species for the family Richtersiidae and a popular laboratory model, exemplifies a common problem in modern tardigrade taxonomy. Despite undeniable progress in the field, many old and incomplete descriptions of taxa hinder both species delimitation and the estimation of species diversity and distribution. Although for over a century this species has been recorded throughout the world, recent research indicates that records to date are likely to represent a species complex rather than a single cosmopolitan species. However, in order to recognise and name species diversity within the complex, an integrative redescription of the nominal species is first needed. Here, we describe an R. coronifer population collected from Spitsbergen, i.e., one of the two localities mentioned in the original description, with detailed morphological and morphometric data associated with standard DNA sequences of four standard genetic markers (18S rRNA, 28S rRNA, ITS-2, and COI) and supported by transcriptome sequencing. We propose replacement of the neotype designated in 1981 by Maucci and Ramazzotti, as it is impossible to verify whether the existing neotype is conspecific with specimens studied by Richters in 1903 and 1904. Finally, using newly obtained cytochrome c oxidase subunit I (COI) sequences of populations from Spitsbergen, Italy, Poland, and Greece together with sequences deposited in GenBank (China, Greenland, Italy, Mongolia), we performed genetic species delimitation, which indicated seven distinct potential species within the genus Richtersius, in addition to the nominal taxon. This study marks a starting point for further research on the taxonomy of and species diversity within the genus. Moreover, this work has the potential to be the first tardigrade redescription to provide both genetic barcodes and a transcriptome of the species in question.

Vegetation affects photoprotective pigments and copepod distribution in the Himalayan lakes: Implication for climate change adaptation

Lakes in the Himalayas host unique biota and biological communities which are highly sensitive to climate change. High penetration of solar UV radiation in clear shallow lake affects the distribution and abundance of the zooplankton communities. Survival of copepods in such habitats often relies on available photoprotective compounds. We estimated species diversity and distribution patterns of copepods with detectable carotenoids in 7 lakes of the central Himalayas along the altitudinal gradients. To determine the factors influencing the accumulation of high-level photoprotective compounds, we analyzed the physicochemical parameters of water and the concentration of Lignin like Compounds (LLCs), Aromaticity (ARO), Humic Compounds (HCs), Degree of Humification (DoH) and percent Total Organic Matter (TOM) in littoral sediments. In the shallow lakes, copepod abundance and diversity correlate with water transparency. Humic compounds (HCs) derived from ligninaceous plants stimulate the accumulation of photoprotective compounds that allow for the domination of diaptomidae. Copepods receive photoprotective compounds from the humic-bounded sediment substrate. The amount of photoprotectants in the aquatic food chain of the central Himalayas is largely influenced by ligninaceous compounds derived from catchment vegetation. In copepods of shallow clear lakes, the remnant of dead trees in the littoral zones helps to minimize hazards caused by exposure effect and climatic stress. The reduction of vegetative covers in the shorelines may alter the community structure of zooplankton, particularly in the upland ecosystem.

Assessing tree species diversity and structure of mixed dipterocarp forest remnants in a fragmented landscape of north-western Borneo, Sarawak, Malaysia

Abstract As forest fragmentation continues in many parts of the tropics, the conservation value of forest remnants remains controversial. Our study aimed to assess the structure and tree species diversity of mixed dipterocarp forest remnants from the Planted Forest Zone (PFZ) located in the Bintulu Division, Sarawak, compared with a forest considered relatively undisturbed (i.e. that has experienced no recent logging activities). We also compared three plot methods (50 × 50 m, 20 × 50 m and 10 × 50 m plots) in order to evaluate which could be used for time- and cost-effective inventories of structure and tree species diversity in fragmented forests. No significant differences were found between the fragmented forests and the relatively undisturbed forest for stem density, species richness and diversity indices (Shannon and Simpson). Dissimilarities in species, genus and family composition were observed between fragmented and relatively undisturbed forest, as well as between forest remnants themselves. These dissimilarities were likely to be related to intrinsic variation in these highly diverse tropical forests. However, an unusually high abundance of pioneer species (i.e. Macaranga) was found in plots from forest remnants. The forest remnants also had significantly lower basal areas due to a lack of trees in large diameter classes, which is likely a result of impacts from past logging activities. Otherwise, our results highlight the current high conservation value of the forest remnants—although the studied communities are likely to experience time-delayed shifts in species composition and/or extinctions in the future, with the effect of fragmentation on biodiversity being currently underestimated. Finally, for further studies of fragmented forests we recommend the use of 10 × 50 m plots which are faster and easier to implement in the field while providing estimates of structure and tree species diversity that are consistent with those from larger plots.

Evolutionary relationships of the ancient fern lineage the adder's tongues (Ophioglossaceae) with description of Sahashia gen. nov.

As an ancient lineage of ferns, Ophioglossaceae are evolutionarily among the most fascinating because they have the highest chromosome count of any known organism as well as the presence of sporophores, subterranean gametophytes, eusporangiate sporangia without annuli, and endophytic fungi. Previous studies have produced conflicting results, identifyingsome lineages with unresolved relationships, and have paid much attention to the subfamily Botrychioideae. But the other species-rich subfamily, Ophioglossoideae, has remained largely understudied and only up to 12 accessions of Ophioglossoideae have been sampled. In this study, DNA sequences of seven plastid markers of 149 accessions (75 in Ophioglossoideae) representing approximately 82 species (approximately 74% of estimated species diversity sensu J. Syst. Evol., 2016, 54, 563) in the family, and two Marattiaceae and two Psilotaceae, are used to infer a phylogeny. Our major results include: (1) Ophioglossaceae are resolved as monophyletic with strong support, and so are all four subfamilies and genera sensu PPG I except Botrypus and Ophioglossum; (2) a new genus Sahashia is segregated from Botrypus so that the monophyly of Botrypus can be retained; (3) the monophyly of Ophioglossum in its current circumscription is uncertain in spite of our large character sampling; (4) there is substantial cryptic speciation in Ophioderma detected by our molecular and morphological study; (5) the recognition of Holubiella is advocated based on its morphology and its sister relationship with Sceptridium; and (6) a novel sister relationship between Botrychium and the JHS clade (Japanobotrychium + (Holubiella+Sceptridium)) is discovered.

Distribution and species diversity of freshwater crabs of the family Pseudothelphusidae in Colombia (Crustacea: Decapoda: Brachyura)

The study of Colombian freshwater crabs has advanced significantly, but species records are scattered across different museums and research institutions. Assuming that museum collections incorporate valuable information in estimating species diversity, a database was organized on the 94 known species of family Pseudothelphusidae, which includes 568 records from 1853 to 2019 in continental Colombia and Gorgona Island. The natural regions of Colombia (Amazonian, Andean, Caribbean, Orinoquian, Pacific) were further subdivided into 75 natural sub-regions according to habitat types used by freshwater crabs. Sub-regions were (i) ranked in terms of species richness, with respective species reported in each sub-region listed accordingly, and (ii) classified into a scale of five categories on the basis of a geometric biodiversity index combining species richness and Simpson index. Species accumulation curves are presented to estimate the current status of knowledge about the diversity of the Colombian pseudothelphusids. Although the available data are not standardized for an adequate assessment of relative abundance, since they are influenced by sampling efforts and natural sub-regions are of different sizes and characteristics, the present study may be useful in future ecological and biogeographic research, as well as for conservation purposes.

Disentangling the evolutionary and biogeographical history of the freshwater fish trematode genus Creptotrema (Digenea: Allocreadiidae) using an integrative taxonomy approach: the case of Creptotrema agonostomi in Middle American mountain mullets.

Species of the allocreadiid genus Creptotrema are parasites of freshwater fishes in the Americas. Species in the genus possess one pair of muscular oral lobes on the oral sucker. Currently, the genus contains eight species, six distributed in South America, one in Middle America and one in North America. Genetic data are only available for the North American species, Creptotrema funduli, a parasite of fundulids originally described from Oneida Lake, New York State. In this study, we obtained 28S ribosomal DNA sequences of trematodes morphologically similar to Creptotrema agonostomi from the mountain mullet, Dajaus monticola, across a wide geographical range in Middle America. Our molecular phylogenetic analyses showed that (1) the genus Creptotrema, as currently conceived, is not monophyletic; (2) the allocreadiids in mountain mullets should be re-allocated in the genus Pseudoparacreptotrema; and (3) the allocreadiid trematodes from D. monticola across Middle America represent four morphologically similar species, three of which can be distinguished genetically. These three new species are described herein using an integrative taxonomy approach. We contend that accurate estimates of species diversity and phylogenetic relationships among allocreadiids, and most likely other species of trematodes, necessarily require an integrative taxonomy approach that should consider at least DNA sequences and scanning electron microscopy.

From marine park to future genomic observatory? Enhancing marine biodiversity assessments using a biocode approach.

Few tropical marine sites have been thoroughly characterised for their animal species, even though they constitute the largest proportion of multicellular diversity. A number of focused biodiversity sampling programmes have amassed immense collections to address this shortfall, but obstacles remain due to the lack of identification tools and large proportion of undescribed species globally. These problems can be partially addressed with DNA barcodes (“biocodes”), which have the potential to facilitate the estimation of species diversity and identify animals to named species via barcode databases. Here, we present the first results of what is intended to be a sustained, systematic study of the marine fauna of Singapore’s first marine park, reporting more than 365 animal species, determined based on DNA barcodes and/or morphology represented by 931 specimens (367 zooplankton, 564 macrofauna including 36 fish). Due to the lack of morphological and molecular identification tools, only a small proportion could be identified to species solely based on either morphology (24.5%) or barcodes (24.6%). Estimation of species numbers for some taxa was difficult because of the lack of sufficiently clear barcoding gaps. The specimens were imaged and added to “Biodiversity of Singapore” (http://singapore.biodiversity.online), which now contains images for > 13,000 species occurring in the country.

Diversity of Earthworms in Nnamdi Azikiwe University, Awka

Abstract Studies reveal that not up to 50% of earthworm species have been described in the world and the understanding of earthworm diversity is finite in most countries including Nigeria. The study was aimed at evaluating the diversity of earthworms and environmental factors affecting their abundance. Earthworms were collected from three (3) different sampling locations in Nnamdi Azikiwe University, Awka. Descriptive statistics and estimation of species abundance, dominance and diversity were used to analyze the data obtained from the study. From the study, four (4) species of earthworms were identified and recorded from the three sampling locations. Eudrilus eugeniae (54.9%) was the most abundant species followed by Hyperidrilus africanus (20.3%), Libyodrilus violaceous (19.6%) and Alma millsoni (6.3%) with the least abundant species. The result of the diversity indices showed Science village (1.13) as the most diverse habitat followed by Emelda hostel (0.86) and Boys’ hostel (0.84) with the least diversity of species. Soil pH ranged from 2.25 to 4.06 and total organic matter ranged from 14.10 to 16.36%. Soil temperature was uniform with an average value of 27°C for the three sampling locations. The soil moisture content ranged from 11.19 to 14.12%. The conductivity recorded the lowest value (25.60μS/cm) in Emelda Hostel and highest value (111.8 μS/cm) in Science village. The study provided understanding into the patterns of earthworm populations in Nnamdi Azikiwe University, Awka and the need for the conservation of earthworm diversity. Better understanding about habitat and living conditions of earthworms is required to provide suitable and enhanced production of vermicompost in different geographic conditions.

Climate-related factors cause changes in the diversity of fish and invertebrates in subtropical coast of the Gulf of Mexico

Climate change impacts physical and chemical properties of the oceans, and these changes affect the ecology of marine organisms. One important ecological consequence of climate change is the distribution shift of marine species toward higher latitudes. Here, the prevalence of nearly 150 species of fish and invertebrates were investigated to find changes in their distributions over 35 years along a subtropical coast within the Gulf of Mexico. Our results show that 90 species increased their occupancy probability, while 33 decreased (remaining species neither increase or decrease), and the ranges of many species expanded. Using rarefaction analysis, which allows for the estimation of species diversity, we show that species diversity has increased across the coast of Texas. Climate-mediated environmental variables are related to the changes in the occupancy probability, suggesting the expansion of tropical species into the region is increasing diversity.

Enhancing DNA metabarcoding performance and applicability with bait capture enrichment and DNA from conservative ethanol.

Metabarcoding is often presented as an alternative identification tool to compensate for coarse taxonomic resolution and misidentification encountered with traditional morphological approaches. However, metabarcoding comes with two major impediments which slow down its adoption. First, the picking and destruction of organisms for DNA extraction are time and cost consuming and do not allow organism conservation for further evaluations. Second, current metabarcoding protocols include a PCR enrichment step which induces errors in the estimation of species diversity and relative biomasses. In this study, we first evaluated the capacity of capture enrichment to replace PCR enrichment using controlled freshwater macrozoobenthos mock communities. Then, we tested if DNA extracted from the fixative ethanol (etDNA) of the same mock communities can be used as an alternative to DNA extracted from pools of whole organisms (bulk DNA). We show that capture enrichment provides more reliable and accurate representation of species occurrences and relative biomasses in comparison with PCR enrichment for bulk DNA. While etDNA does not permit to estimate relative biomasses, etDNA and bulk DNA provide equivalent species detection rates. Thanks to its robustness to mismatches, capture enrichment is already an efficient alternative to PCR enrichment for metabarcoding and, if coupled to etDNA, is a time-saver option in studies where presence information only is sufficient.

A global plastid phylogeny of the fern genus Asplenium (Aspleniaceae).

The infrageneric relationships and taxonomy of the largest fern genus, Asplenium (Aspleniaceae), have remained poorly understood. Previous studies have focused mainly on specific species complexes involving a few or dozens of species only, or have achieved a large taxon sampling but only one plastid marker was used. In the present study, DNA sequences from six plastid markers (atpB, rbcL, rps4, rps4-trnS, trnL and trnL-F) of 1030 accessions (616 of them newly sequenced here) representing c. 420 species of Asplenium (60% of estimated species diversity), 16 species of Hymenasplenium, three Diplaziopsidaceae, and four Rhachidosoraceae were used to produce the largest genus-level phylogeny yet for ferns. Our major results include: (i) Asplenium as broadly circumscribed is monophyletic based on our inclusion of representatives of 32 of 38 named segregate genera; (ii) 11 major clades in Asplenium are identified, and their relationships are mostly well-resolved and strongly supported; (iii) numerous species, unsampled in previous studies, suggest new relationships and numerous cryptic species and species complexes in Asplenium; and (iv) the accrued molecular evidence provides an essential foundation for further investigations of complex patterns of geographical diversification, speciation and reticulate evolution in this family.

Hidden in plain sight: how overlooking ephemeral bryophytes can bias biodiversity assessments and conservation actions

Biodiversity assessments are currently routine in most countries for measuring the impact of environmentally damaging projects. In order to properly document the species diversity occurring at a given locality, a fine understanding of the life history of each taxonomic group is needed. Thus, organism groups whose life cycle is poorly known may be overlooked in floristic assessments and underrepresented in natural history collections. This may lead to incomplete sampling and eventually inappropriate estimates of the local diversity and the extinction risks of certain taxa. Here, we study ephemeral bryophytes in central Chile semi-arid ecosystems. We selected Costesia macrocarpa, a Chilean endemic moss, as a model to demonstrate the consequences of omitting the life cycle information of a taxon when assessing its extinction risk, and for plant species diversity estimation in a given area. Based on winter sampling, we found that Costesia is not a vulnerable nor a nearly-threatened taxon, as has been previously suggested. Our findings reveal that it is ubiquitous throughout central Chile during the wet season, with no observed risk of extinction. These observations can be applied to several other little-known ephemeral bryophyte taxa found in central Chile.

Effects of inventory grids on estimation of tree species diversity in semi-arid forests of Iran

Abstract Species diversity is one of the most important indices used to evaluate the sustainability of forest communities. The sampling method and the number of plots are factors affecting the estimation of plant biodiversity. In the present study, effects of different inventory grids on estimation of tree species diversity were compared in semi-arid forests of Iran. There were selected 50 hectares of these forests representing the regional forests. Sampling procedures were carried out on circular plots (1,000m2) within inventory grids, with dimensions of 50 × 50 m (200 plots), 100 × 50 m (100 plots), 100 × 100 m (50 plots), 200 × 50 m (50 plots), 200 × 100 m (25 plots), and 250 × 200 m (10 plots). For each plot, the type of the species and the number of trees were recorded. Simpson (1-D), Hill (N2), Shannon-Wiener (H’), Mc Arthur (N1), Smith-Wilson (Evar) and Margalef (R1) indices were used to estimate the tree species diversity. The inventory grid was evaluated based on the precision and cost criteria (E%2 × T). The obtained sampling error values showed that the inventory grid consisting of 200 plots exhibited more accuracy for estimating the biodiversity indices. But based on the results of E%2 × T, the inventory grid with 25 plots was selected as the most appropriate one for estimating the tree species diversity in semi-arid forests. The results of this study can also serve to estimate the tree species diversity in other semi-arid forests of Iran.

Estimating tree species diversity from space in an alpine conifer forest: The Rao's Q diversity index meets the spectral variation hypothesis

Forests cover about 30% of the Earth surface, they are among the most biodiverse terrestrial ecosystems and represent the bulk of many ecological processes and services. The assessment of biodiversity is an important and essential goal to achieve but it can results difficult, time consuming and expensive when based on field data. Remote sensing covers large areas and provides consistent quality and standardized data, which can be used to estimate species diversity. One method to estimate species diversity from remote sensing data is based on the Spectral Variation Hypothesis (SVH), which assumes that the higher the spectral variation of an image, the higher the environmental heterogeneity and the species diversity of the considered area. SVH has been tested using different spectral heterogeneity (SH) indices and measures, recently the Rao's Q index has been proposed as a new spectral variation measure to be applied to remote sensing data. In this paper, we tested the SVH in an alpine coniferous forest to estimate tree species diversity. We evaluated the performance of the Rao's Q index and compared it with another widely used SH index, the Coefficient of Variation (CV), validating them against values of Shannon's H (used as species diversity index) derived from in-situ collected data. A NDVI time-series (for 2016 and 2017) derived from the Sentinel-2A and 2B and Landsat 8 OLI satellites has been used to test the effect of the spatial grain of both the sensors and to understand the seasonality of the SVH. The results showed that the SVH is season and sensor dependent. For both years and satellites, the relation between Rao's Q and field data reached the highest R2 between June and July, decreasing towards winter and spring similarly to the NDVI time-series. This relationship could be given because, when NDVI reaches its highest values, it is able to capture small variation in reflectance of different leaf traits typical of specific trees. The relation between field and spectral diversity reached a value of R2 = 0.70 (2017) and R2 = 0.48 (2016) for Sentinel-2 and of R2 = 0.42 (2017) and R2 = 0.47 (2016) for Landsat 8. CV showed the same NDVI temporal tendency. However, the relation between field-derived Shannon's H and CV was on average lower than that we found for Rao's Q. This research underlined the goodness of the Rao's Q index, the relevance of the NDVI in the study of the SVH and the importance of the multi-temporal approach.

Reproductive isolation, morphological and ecological differentiation among cryptic species of Euchlanis dilatata, with the description of four new species

Morphological approaches may not provide sufficient resolution for species delineation. Thus, we used an integrated approach that included molecular and ecological characters as well as morphological features to gain a better estimate of species diversity and to improve our understanding of the speciation process within rotifers. Previously, seven putative cryptic species were found within Euchlanis dilatata complex based on a nuclear marker. Here, we investigated reproductive isolation, variation in trophi morphology, and life history characteristics among representatives of some of these species. Mating success between each cryptic species was 0–1.1%; lower than that of positive controls (intra-clonal: 15.6–43.9%). SEM trophi images representing individuals from all seven lineages were used for morphometric analyses. Using Discriminant Analysis, 64% of individuals were correctly assigned to cryptic species. Five clonal lineages, each representing a putative species, were used in life table experiments with varying temperature and conductivity. Age-specific fecundity increased under high temperature and life expectancy decreased under high temperature and high conductivity. There was variation among cryptic species in some life table characteristics, such as life expectancy and generation time. Applying an integrative taxonomy approach, we examined the boundaries between E. dilatata cryptic species and described four of them as new species.

Combining high resolution satellite imagery and lidar data to model woody species diversity of tropical dry forests

Tropical dry forests provide goods and ecosystem services that rely on their diversity and are vital for human wellbeing. However, they are among the most threatened ecosystems due mainly to conversion to agriculture. Accurate estimations of species diversity in tropical secondary forests are needed for effective conservation and forest management. We assessed the separate and combined performance of remotely-sensed surrogates of habitat heterogeneity and vegetation structure complexity for predicting and mapping woody plant species richness and diversity in tropical dry forests. Here, we used image texture measures to calculate spectral variability from RapidEye imagery as an indicator of habitat heterogeneity as well as height and cover metrics from LiDAR data as surrogates of the complexity of vegetation structure. Separately, image texture measures and LiDAR metrics were used to explain variation in species richness and exp Shannon diversity calculated in 48 plots using multiple regression analysis. We also evaluated the relative importance of two sets of indicators to estimate species diversity using variation partitioning analyses. Habitat heterogeneity (image texture metrics) contributed most to explain variation in species richness (R2: 0.72–0.87), whereas complexity of vegetation structure (LiDAR metrics) was more important for diversity (R2: 0.68–0.74). However, a large percentage of variance of richness and diversity (58%–67%) was jointly explained by both factors and using models that combine them provided similar or higher prediction accuracy (R2: 0.68–0.89). We conclude that using image texture of high resolution imagery as an indicator of habitat heterogeneity allows precise and cost-effective estimations of species richness, while LiDAR metrics as a surrogate of vegetation structure complexity allow better estimations of diversity and that combining image texture and LiDAR provides the best estimates of species richness and diversity.

Richness, diversity, and factors influencing occupancy of mammal communities across human-modified landscapes in Colombia

As human-modified landscapes are increasing in the tropics, it becomes critical to understand how they affect mammal communities to reconcile conservation and development. We combined land cover information and camera-trapping data to explore the effects of agricultural expansion on mammals in the Magdalena river valley of Colombia. We estimated species diversity, evenness, and dominance across two agricultural landscapes, modified by cattle ranching and oil palm cultivation. We further assessed which variables influence species- and community-level occupancy using multi-species occupancy models. Results highlight that modified landscapes display lower species richness, diversity and evenness, and higher dominance than more pristine sites. Residual forest cover and distance to water had significant effect on community occupancy (positive and negative respectively). Forests were particularly important for pumas, ocelots, lowland pacas, Central American agoutis, and crab-eating raccoons while wetlands had a positive effect on jaguars, the apex predator in the region. The influence of anthropogenic pressure was not clearly evident, though pastures were not valuable habitats for any mammal species, as they had a negative, yet not significant, effect on species and community occupancy. In light of rapidly expanding agriculture across the tropics, our findings highlight species-specific responses to disturbance that can inform land use planning and conservation policies. We stress the conservation value of forest and wetland habitat to mammal occupancy in heterogeneous ecosystems. Moreover, our results demonstrate that oil palm and crop expansion should target existing pastures, which displayed limited conservation value for Neotropical mammals but occupy vast swathes of land across Latin America.