Message in a Bottle, Metabarcoding Enables Biodiversity Comparisons Across Ecoregions

Background Traditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large scale assessments required to manage and protect entire ecosystems. This study employed DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52 protected areas spanning three Canadian ecoregions. Results This study revealed the presence of 26,263 arthropod species in the three ecoregions and indicated that at least another 3,000 to 5,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall alphadiversity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site with turnover greater than nestedness, suggesting the presence of many transient species. Conclusions Differences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric employed in prior efforts to track change in arthropod communities.

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Repeated surveying over 6 years reveals that fine-scale habitat variables are key to tropical mountain ant assemblage composition and functional diversity

Scientific Reports ◽

10.1038/s41598-020-80077-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mulalo M. Muluvhahothe ◽

Grant S. Joseph ◽

Colleen L. Seymour ◽

Thinandavha C. Munyai ◽

Stefan H. Foord

Keyword(s):

Climate Change ◽

Species Composition ◽

High Altitude ◽

Functional Diversity ◽

Large Scale ◽

Climate Models ◽

Spatial Scales ◽

Abiotic Factors ◽

Composition Analysis ◽

Fine Scale

AbstractHigh-altitude-adapted ectotherms can escape competition from dominant species by tolerating low temperatures at cooler elevations, but climate change is eroding such advantages. Studies evaluating broad-scale impacts of global change for high-altitude organisms often overlook the mitigating role of biotic factors. Yet, at fine spatial-scales, vegetation-associated microclimates provide refuges from climatic extremes. Using one of the largest standardised data sets collected to date, we tested how ant species composition and functional diversity (i.e., the range and value of species traits found within assemblages) respond to large-scale abiotic factors (altitude, aspect), and fine-scale factors (vegetation, soil structure) along an elevational gradient in tropical Africa. Altitude emerged as the principal factor explaining species composition. Analysis of nestedness and turnover components of beta diversity indicated that ant assemblages are specific to each elevation, so species are not filtered out but replaced with new species as elevation increases. Similarity of assemblages over time (assessed using beta decay) did not change significantly at low and mid elevations but declined at the highest elevations. Assemblages also differed between northern and southern mountain aspects, although at highest elevations, composition was restricted to a set of species found on both aspects. Functional diversity was not explained by large scale variables like elevation, but by factors associated with elevation that operate at fine scales (i.e., temperature and habitat structure). Our findings highlight the significance of fine-scale variables in predicting organisms’ responses to changing temperature, offering management possibilities that might dilute climate change impacts, and caution when predicting assemblage responses using climate models, alone.

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Genetic and morphological diversity of the cosmopolitan chaetognath Pseudosagitta maxima (Conant, 1896) in the Atlantic Ocean and its relationship with the congeneric species

ICES Journal of Marine Science ◽

10.1093/icesjms/fsw255 ◽

2017 ◽

Vol 74 (7) ◽

pp. 1875-1884 ◽

Cited By ~ 2

Author(s):

Dmitry N. Kulagin ◽

Tatiana V. Neretina

Keyword(s):

Atlantic Ocean ◽

Large Scale ◽

Phylogenetic Analyses ◽

Morphological Diversity ◽

Maturity Stage ◽

Congeneric Species ◽

Morphological Examination ◽

Posterior Teeth ◽

Biogeographic Patterns ◽

True Diversity

Abstract Until recently many oceanic zooplankton species have been considered as cosmopolitan organisms. At present it became evident that some of them comprise many distinct molecular operational taxonomic units (MOTUs) that often are regarded as cryptic species. As they can significantly change our perceptions of large-scale biogeographic patterns, it is important to characterize the true diversity within common and ecologically important groups. We have analysed the molecular and morphological diversity of the cosmopolitan mesopelagic chaetognath Pseudosagitta maxima throughout the Atlantic Ocean from 60° S to 85° N and its position within the genus Pseudosagitta. Three distinct mitochondrial clades within P. maxima were revealed with phylogenetic analyses (Maximum Likelihood, Bayesian Inference) and were geographically separated. The subsequent analyses of nuclear markers (H3, ITS1) have shown that P. maxima most likely comprises two distinct MOTUs, tropical and bipolar, that also have some morphological differences. The latter MOTU consists of two genetically slightly divergent populations: southern and northern. The morphological examination allowed the determination of a character (type of hook coloration) that accurately distinguishes juveniles of the P. maxima complex from the other congeneric species. Molecular data have shown that evolutionary P. lyra and P. gazellae are more closely related to each other than to P. maxima. Number of hooks, number of anterior and posterior teeth and the arrangement of ova in the ovary were proposed to be the most useful morphological characters to distinguish between tropical and bipolar MOTUs within the P. maxima complex. The first three characters should be determined for each maturity stage separately.

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Ecological processes maintaining differential tree species distributions in an Australian subtropical rain forest: implications for models of species coexistence

Journal of Tropical Ecology ◽

10.1017/s0266467400001474 ◽

2000 ◽

Vol 16 (3) ◽

pp. 387-415 ◽

Cited By ~ 20

Author(s):

Igor Debski ◽

David F. R. P. Burslem ◽

David Lamb

Keyword(s):

Species Composition ◽

Tree Species ◽

Rain Forest ◽

Large Scale ◽

Species Coexistence ◽

Common Species ◽

Size Class ◽

Differential Mortality ◽

Mixed Composition ◽

Large Scale Disturbance

All stems ≥ 1 cm dbh were measured, tagged, mapped and identified on a 1-ha plot of rain forest at Gambubal State Forest, south-east Queensland, Australia. The spatial patterns and size class distributions of 11 common tree species on the plot were assessed to search for mechanisms determining their distribution and abundance. The forest was species-poor in comparison to many lowland tropical forests and the common species are therefore present at relatively high densities. Despite this, only limited evidence was found for the operation of density-dependent processes at Gambubal. Daphnandra micrantha saplings were clumped towards randomly spaced adults, indicating a shift of distribution over time caused by differential mortality of saplings in these adult associated clumps. Ordination of the species composition in 25-m × 25-m subplots revealed vegetation gradients at that scale, which corresponded to slope across the plot. Adult basal area was dominated by a few large individuals of Sloanea woollsii but the comparative size class distributions and replacement probabilities of the 11 common species suggest that the forest will undergo a transition to a more mixed composition if current conditions persist. The current cohort of large S. woollsii individuals probably established after a large-scale disturbance event and the forest has not attained an equilibrium species composition.

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Do arthropod assemblages fit the grassland and savanna biomes of South Africa?

South African Journal of Science ◽

10.17159/sajs.2016/20150424 ◽

2016 ◽

Vol Volume 112 (Number 9/10) ◽

Cited By ~ 7

Author(s):

Monique Botha ◽

Stefan J. Siebert ◽

Johnnie van den Berg ◽

◽

...

Keyword(s):

South Africa ◽

Multidimensional Scaling ◽

Vegetation Structure ◽

Species Assemblages ◽

Trophic Groups ◽

Arthropod Communities ◽

Arthropod Species ◽

Scaling Analyses ◽

Suction Sampling ◽

Functional Assemblages

Abstract The long-standing tradition of classifying South Africa’s biogeographical area into biomes is commonly linked to vegetation structure and climate. Because arthropod communities are often governed by both these factors, it can be expected that arthropod communities would fit the biomes. To test this hypothesis, we considered how well arthropod species assemblages fit South Africa’s grassy biomes. Arthropod assemblages were sampled from six localities across the grassland and savanna biomes by means of suction sampling, to determine whether the two biomes have distinctive arthropod assemblages. Arthropod samples of these biomes clustered separately in multidimensional scaling analyses. Within biomes, arthropod assemblages were more distinctive for savanna localities than grassland. Arthropod samples of the two biomes clustered together when trophic groups were considered separately, suggesting some similarity in functional assemblages. Dissimilarity was greatest between biomes for phytophagous and predacious trophic groups, with most pronounced differentiation between biomes at sub-escarpment localities. Our results indicate that different arthropod assemblages do fit the grassy biomes to some extent, but the pattern is not as clear as it is for plant species.

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Global biogeographic patterns in bipolar moss species

Royal Society Open Science ◽

10.1098/rsos.170147 ◽

2017 ◽

Vol 4 (7) ◽

pp. 170147 ◽

Cited By ~ 23

Author(s):

E. M. Biersma ◽

J. A. Jackson ◽

J. Hyvönen ◽

S. Koskinen ◽

K. Linse ◽

...

Keyword(s):

Large Scale ◽

Common Species ◽

Long Distance Dispersal ◽

Stepping Stones ◽

Long Distance ◽

Antarctic Region ◽

Moss Species ◽

Biogeographic Patterns ◽

Biogeographic Pattern ◽

The Antarctic

A bipolar disjunction is an extreme, yet common, biogeographic pattern in non-vascular plants, yet its underlying mechanisms (vicariance or long-distance dispersal), origin and timing remain poorly understood. Here, combining a large-scale population dataset and multiple dating analyses, we examine the biogeography of four bipolar Polytrichales mosses, common to the Holarctic (temperate and polar Northern Hemisphere regions) and the Antarctic region (Antarctic, sub-Antarctic, southern South America) and other Southern Hemisphere (SH) regions. Our data reveal contrasting patterns, for three species were of Holarctic origin, with subsequent dispersal to the SH, while one, currently a particularly common species in the Holarctic ( Polytrichum juniperinum ), diversified in the Antarctic region and from here colonized both the Holarctic and other SH regions. Our findings suggest long-distance dispersal as the driver of bipolar disjunctions. We find such inter-hemispheric dispersals are rare, occurring on multi-million-year timescales. High-altitude tropical populations did not act as trans-equatorial ‘stepping-stones’, but rather were derived from later dispersal events. All arrivals to the Antarctic region occurred well before the Last Glacial Maximum and previous glaciations, suggesting that, despite the harsh climate during these past glacial maxima, plants have had a much longer presence in this southern region than previously thought.

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Adult caddisflies (Trichoptera) attracted to artificial lights in the middle reaches of the Shinano River from 2005 to 2007

Zoosymposia ◽

10.11646/zoosymposia.5.1.12 ◽

2011 ◽

Vol 5 (1) ◽

pp. 143-146 ◽

Cited By ~ 2

Author(s):

KIMIO HIRABAYASHI ◽

GORO KIMURA ◽

EISO INOUE

Keyword(s):

Species Composition ◽

Air Temperature ◽

Large Scale ◽

Abundant Species ◽

The Other ◽

Seasonal Abundance ◽

Other Hand ◽

The Mean ◽

Summer Flood

The species composition and abundance of adult caddisflies attracted to the illuminated showcase of a vending machine set along the middle reaches of the Shinano River were investigated every Sunday night from April to November in 2005 to 2007. A total of 1,405 adult caddisflies was collected during the investigation periods. We identified a total of 13 species belonging to 11 genera of 8 families. The most abundant species was Psychomyia acutipennis (Ulmer 1908) each year. Psychomyia acutipennis adults were collected from mid-May to the beginning of October (the range of mean air temperature was 13.8 to 27.7°C), with its seasonal abundance divided into several peaks, i.e., the end of May, the beginning of June, and the end of August to the beginning of September in both 2006 and 2007. On the other hand, in 2005 when there was no large-scale summer flood and there were no marked abundance peaks. The present study suggests that the mean air temperature and summer floods impacted the seasonal abundance of P. acutipennis adults.

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Ground-dwelling arthropod (Araneae, Coleoptera: Carabidae, Isopoda: Oniscidea) assemblages on Hungarian main road verges

Acta Universitatis Sapientiae Agriculture and Environment ◽

10.1515/ausae-2016-0009 ◽

2016 ◽

Vol 8 (1) ◽

pp. 96-111

Author(s):

Diána Vona-Túri ◽

Tünde Szmatona-Túri ◽

Ferenc Kádár ◽

Balázs Kiss ◽

András Weiperth ◽

...

Keyword(s):

Species Composition ◽

Red List ◽

Agricultural Area ◽

Dominance Relation ◽

Beetle Species ◽

Arthropod Communities ◽

Main Road ◽

Spider Species ◽

Road Verges ◽

Diverse Habitat

Abstract In this study, we research ground-dwelling arthropods along four road stretches, which represent the main verge habitats (arid grassland, agricultural area, forest, and wetland) of Hungary. Besides the faunistic investigation of arthropod communities, we described and compared dominance relation and species composition. We identified 83 carabids, 81 spiders, and 4 isopod species. Seven beetle species and one spider species are included in the invertebrate Red List of Hungary. The registered species were dominant on main road verges bordering arid grassland and wetland. Main road verges proved to be a diverse habitat; hence, it is important to carry on more investigation.

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Development of forest soils in the Krkonoše Mts. in the period 1980–2009

Journal of Forest Science ◽

10.17221/79/2010-jfs ◽

2010 ◽

Vol 56 (No. 11) ◽

pp. 485-504 ◽

Cited By ~ 5

Author(s):

K. Matějka ◽

S. Vacek ◽

V. Podrázský

Keyword(s):

Species Composition ◽

Tree Species ◽

Large Scale ◽

Vegetation Change ◽

Soil Conditions ◽

Available Phosphorus ◽

Mountain Range ◽

Site Conditions ◽

Tree Species Composition ◽

Spruce Stands

This paper documents the development of soil conditions in the set of 32 permanent research plots in the Krkono&scaron;e (Giant) Mts. These plots represent an altitudinal gradient covering the ecosystems of beech, mixed beech-spruce and spruce stands. In all plots, representing the site conditions of the highest areas of the mountain range, standard soil pits were prepared and the soil sampling was performed in autumn of years 1980, 1993, 1998, 2003 and 2009. The results reflect extreme site conditions, soil acidification, large scale surface liming and in minor extent also different tree species composition of the stands. The general type of the soil-genesis is represented by the podzolisation, overlapping the other soil-genetic factors, including the tree species composition. Nevertheless, this development is mostly expressed in the spruce stands. The beech dominance and/or co-dominance are reflected especially by more efficient N-cycling, higher pH, S and V values and fluctuation and lower extractable Al3+ content. More efficient cycling in beech ecosystems is insignificantly documented for plant available phosphorus, calcium and magnesium contents; on the contrary higher dynamics for iron ions was registered in the spruce stands. The long-term soil dynamics with a hysteresis (evident on the base of ordination analysis) can be divided into some periods – processes of acidification (typical in the 1980's samples), liming (main effect in 1993 and 1998) and regeneration (2003, 2009). Other features, important for the soil development, are probably related to the vegetation change, but this relation is not statistically significant.

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Monitoring Post-Fire Recovery of Chaparral and Conifer Species Using Field Surveys and Landsat Time Series

Remote Sensing ◽

10.3390/rs11242963 ◽

2019 ◽

Vol 11 (24) ◽

pp. 2963

Author(s):

Christopher L. Kibler ◽

Anne-Marie L. Parkinson ◽

Seth H. Peterson ◽

Dar A. Roberts ◽

Carla M. D’Antonio ◽

...

Keyword(s):

Remote Sensing ◽

Time Series ◽

Land Cover ◽

Species Composition ◽

Vegetation Cover ◽

Spatial And Temporal Variation ◽

Conifer Species ◽

Burn Scar ◽

Green Vegetation ◽

Normalized Burn Ratio

Recovery trajectories derived from remote sensing data are widely used to monitor ecosystem recovery after disturbance events, but these trajectories are often retrieved without a precise understanding of the land cover within a scene. As a result, the sources of variability in post-disturbance recovery trajectories are poorly understood. In this study, we monitored the recovery of chaparral and conifer species following the 2007 Zaca Fire, which burned 97,270 ha in Santa Barbara County, California. We combined field survey data with two time series remote sensing products: the relative delta normalized burn ratio (RdNBR) and green vegetation (GV) fractions derived from spectral mixture analysis. Recovery trajectories were retrieved for stands dominated by six different chaparral species. We also retrieved recovery trajectories for stands of mixed conifer forest. We found that the two remote sensing products were equally effective at mapping vegetation cover across the burn scar. The GV fractions (r(78) = 0.552, p < 0.001) and normalized burn ratio (r(78) = 0.555, p < 0.001) had nearly identical correlations with ground reference data of green vegetation cover. Recovery of the chaparral species was substantially affected by the 2011–2017 California drought. GV fractions for the chaparral species generally declined between 2011 and 2016. Physiological responses to fire and drought were important sources of variability between the species. The conifer stands did not exhibit a drought signal that was directly correlated with annual precipitation, but the drought likely delayed the return to pre-fire conditions. As of 2018, 545 of the 756 conifer stands had not recovered to their pre-fire GV fractions. Spatial and temporal variation in species composition were important sources of spectral variability in the chaparral and conifer stands. The chaparral stands in particular had highly heterogeneous species composition. Dominant species accounted for between 30% and 53% of the land cover in the surveyed chaparral patches, so non-dominant land cover types strongly influenced remote sensing signals. Our study reveals that prolonged drought can delay or alter the post-fire recovery of Mediterranean ecosystems. It is also the first study to critically examine how fine-scale variability in land cover affects time series remote sensing analyses.

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