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opencc-zeroFeb 2023View details →

Conservation prioritisation through genomic reconstruction of demographic histories applied to two endangered suids in the Malay Archipelago

Aim: The biodiversity of the Malay Archipelago is the product of the region's rich biogeographical history with periods of island connectivity and isolation during the Pleistocene glacial cycles. Here, the case of two endemic suid species, the Javan (Sus verrucosus) and Bawean (S. blouchi) warty pigs, was used to illustrate how biogeographic processes and recent anthropogenic pressures can shape demographic histories with significant implications for species conservation. Location: Malay Archipelago, with focus on Bawean and Java. Methods: We employed genome-wide single nucleotide polymorphisms from the Porcine SNP60 v2 BeadChip to assess interspecific genetic differentiation, to estimate divergence times, and to perform demographic model selection. Results: In contrast to the hypothesis of recent divergence during the last glacial maximum, S. blouchi was found to have diverged from S. verrucosus at least 166k years ago following a founder event. The contemporary S. blouchi population was characterised by a recent bottleneck that reduced the effective population size to less than 20. The genomic assessment supports the single species status of S. blouchi, as was previously proposed based on morphometrics. The demographic history of S. verrucosus showed evidence of secondary contact with the sympatric banded pig (S. scrofa vittatus) that colonised Java 70k years ago. Main conclusions: While the Javan and Bawean warty pigs have persisted throughout the Pleistocene climatic oscillations, contemporary pressures from human activities threaten their survival and immediate action should be taken to grant legal protection to both S. verrucosus and S. blouchi. This study highlighted the use of demographic history modelling using genomic data to identify evolutionary significant units and inform conservation.

opencc-by-4.0May 2022View details →

Field margins as substitute habitat for the conservation of birds in agricultural wetlands; Supplementary information

Supplementary material, dataset and script links to the research paper submit for recommendation by PCI Ecology.

opencc-by-4.0Feb 2023View details →

Data supplement for PhD thesis "Pattern Formation with Mass Conservation - From Passive to Active Models"

Here, we provide Mathematica files that provide the details of the weakly nonlinear analysis employed in the PhD thesis "Pattern Formation with Mass Conservation - From Passive to Active Models" submitted by Tobias Frohoff-Hülsmann.

opencc-zeroMar 2023View details →

Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird

Genetic data can be highly informative for answering questions relevant to practical conservation efforts but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote, and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.

Figure 5 in Diversity and conservation of fishes from karstic areas of the Jandaíra Formation in the Brazilian semiarid

Figure 5. Examples of fishes recorded in the Apodi-Mossoró river basin, Jandaíra formation karst, Rio Grande do Norte State, Brazil. (A) Hoplerythrinus unitaeniatus, (B) Trachelyopterus galeatus, (C) Cichla sp., (D) Astyanax bimaculatus, (E) Hypostomus pusarum, (F) Cichlasoma orientale, (G) Characidium bimaculatum, (H) Loricariichthys derbyi and (I) Oreochromis niloticus.

Figure 6 in Diversity and conservation of fishes from karstic areas of the Jandaíra Formation in the Brazilian semiarid

Figure 6. Hoplias malabaricus (bottom right), shoal of Astyanax bimaculatus, and Poecilia vivipara in a shallow waterhole at site 12 in the Carmo river.

Figure 4 in Diversity and conservation of fishes from karstic areas of the Jandaíra Formation in the Brazilian semiarid

Figure 4. Graphic representation of fish by orders (A), and fish richness in each sampling site (B). * Located in the Furna Feia National Park.

Figure 1 in Diversity and conservation of fishes from karstic areas of the Jandaíra Formation in the Brazilian semiarid

Figure 1. Map of the sampling sites in the karstic Jandaíra Formation (dark gray areas), Rio Grande do Norte State, Northeast Brazil. Dark blue lines indicate hydrography. Green shape shows the limits of the Furna Feia National Park. Circles represent temporary water bodies and triangles represent perennial localities. Surface sites are show in red, those associated to caves in orange, and caves in yellow.

Figure 2 in Diversity and conservation of fishes from karstic areas of the Jandaíra Formation in the Brazilian semiarid

Figure 2. Examples of sampling sites in karstic areas of the Jandaíra Formation in Rio Grande do Norte State, Brazil. Surface habitats of sites 5, 11 and 18 (A, B and C), habitats associated to caves of sites 13 (D and E) and 14 (F), cave habitats of sites 16, 17 and 22 (G, H and I).

opencc-by-4.0Mar 2023View details →

Dung Beetle Diversity Survey Data for Sekar Imej Conservation Area (SICA)

The Sekar Imej Conservation Area (SICA) project was initiated by Wilmar International with aims, (1) Establishing effective management of High Conservation Value (HCV) for long term biodiversity conservation in plantation landscapes; (2) capacity building to support local communities; and (3) empowering local communities to support the protection within SICA landscapes. The SICA is recognised as the largest conservation area (2,469 hectares) within Wilmar’s operations in Malaysia (Forest & Reserves, 2021). A rapid assessment was conducted to assess the diversity of dung beetles within the targeted trails. Fieldwork was conducted from 26th – 29th September 2022. Dung beetle sampling was carried out in Monjuk trail (117°11’07.0’’; 6°20’54.1’’) and Tobobon trail (117°11’42.5’’; 6°21’14.5’’) at Sekar Imej Conservation Area (SICA), Sabah, Malaysian Borneo. The forest consist of secondary forest, dominated area with young regenerating forest and lowland mixed dipterocarp forest. These trails are located nearby to larger Paitan and Lingkabau Forest Reserves, which interspersed between other oil palm plantations. We did pitfall and canopy traps using human dung, trapping for 48 hours. The traps were spaced 200 metres from one another.

opencc-zeroMar 2023View details →

Temperature drives the coordination between aboveground nutrient conservation and belowground nutrient acquisition in alpine coniferous forests

Aboveground nutrient conservation via resorption processes and belowground nutrient acquisition from soils are two important mechanisms for plants to maintain nutrition and ecosystem functions. However, the mechanism by which plants coordinate these two nutrient strategies, especially for ectomycorrhizal (ECM)-dominated conifers in alpine forests, remains unclear. We investigated the relationships between aboveground nutrient conservation and belowground nutrient acquisition and their environmental drivers by measuring leaf nutrient (i.e., nitrogen [N] and phosphorous [P]) resorption efficiency, resource foraging- and uptake-related root morphological (root diameter [RD], specific root length [SRL]/area [SRA]) and physiological (root tissue density [RTD], root N and P concentration) traits, mycorrhizal colonization rate (MCR), rhizosphere effect on soil N and P cycling, and environmental factors of 40 ECM coniferous populations on the eastern Tibetan Plateau, China. Our results show that with increasing leaf nutrient (N and P) resorption efficiency, conifers shifted from depending on the 'outsourcing' strategy by mycorrhizal fungi (high MCR) to relying on the 'do-it-yourself' strategy of root mining (high rhizosphere effect on N- and P-mining-related enzyme activities) rather than on root foraging (high SRL and SRA) and preferred more conservative roots (high RTD and low root N and P concentrations). Temperature was the main factor driving a negative relationship of ECM fungi foraging, root uptake and a positive relationship of root mining with leaf nutrient resorption, while precipitation resulted in a decoupled relationship between root foraging and leaf nutrient resorption. Our findings demonstrate temperature-driven and diverse collaborations (e.g., tradeoff or synergy) between belowground nutrient acquisition and aboveground nutrient conservation strategies in alpine ECM conifers and highlight that the preference for belowground nutrient acquisition strategies could influence the aboveground nutrient utilization strategy. This is insightful for a holistic understanding of the adaptation and responses of alpine forests to climatic change.

opencc-zeroMar 2023View details →

Data from: Monitoring temporal and spatial trends of illegal and legal fishing in Canada's marine conservation areas using vessel tracking datasets

Expansion of marine conservation areas (CA) necessitates resource-efficient and achievable strategies for monitoring and evaluation of ongoing fishing activity at national levels. To demonstrate and explore such a strategy, we conducted the first extensive analysis of fishing activity within Canada's static, geographically defined marine CAs with fishing regulations (n = 264 areas). We used eight years of Automatic Identification System data to estimate fishing effort across three oceans and conducted temporal and spatial comparisons specific to each CA's regulations and enactment date. We addressed questions on CA effectiveness, fishing displacement, fishing the line behavior, and relationships between fishing activity and spatial CA attributes. We estimated 22,000 hours of fishing activity within CAs after enactments, 22% of which was identified as illegal. CA effectiveness appeared to be lowest for Atlantic CAs based on illegal fishing effort density within CAs. Fishing displacement and fishing the line was generally not apparent as buffer areas around CAs tended to already have higher fishing effort prior to enactments. CA effectiveness and responses to CAs varied considerably, as was visualized using timeseries plots and maps developed for each CA. Our evaluation of a nation's full suite of CAs provides managers with a foundation and approach for continued monitoring and reporting.

A plea for scale, and why it matters for invasive species management, biodiversity, and conservation

<ol> <li>Invasive species are suspected to be major contributors to biodiversity declines worldwide. Counterintuitively, however, invasive species effects are likely scale-dependent, and are hypothesized to be positively related to biodiversity at large spatial scales. Past studies investigating the effect of invasion on biodiversity have been mostly conducted at small scales (<100 m2) that cannot represent large-dynamic landscapes by design. Therefore, replicated experimental evidence supporting a negative effect of invasive plants on biodiversity is lacking across many landscape types, including large grasslands.</li> <li>We collected data across eight large (333–809 ha) grassland landscapes managed with pyric herbivory—i.e., the recoupling of fire and grazing—to test how an invasive legume (Lespedeza cuneata) affected plant and bird communities at spatial grains ranging from 0.1 m2 to >3,000,000 m2.</li> <li> L. cuneata invasion effects on grassland plant diversity and composition changed with scale; being negative at small spatial grains (0.1 m2) and neutral or positive at large spatial grains (>3,000,000 m2).</li> <li> L. cuneata abundance did not significantly affect bird diversity at any spatial grain measured.</li> <li> L. cuneata may negatively affect biodiversity if abundances are greater than those observed in this study. However, previous research suggests that L. cuneata may not be capable of exceeding 20% canopy cover across large landscapes (>400 ha). Control and eradication strategies can be costly and are fraught with risk. If data do not clearly support a negative L. cuneata abundance-biodiversity relationship, and if invasion is spatially limited across large landscapes, ongoing control and eradication efforts may be unwarranted and ineffective.</li> <li> Synthesis and applications: Invasive species effects gleaned from small-scale studies may not reliably predict their effects at larger scales. Although we recognize the importance of small-scale studies in potentially isolating individual mechanisms, management strategies based solely on results from small-scale studies of invasion are unlikely to increase or conserve biodiversity across large landscapes. Rather, processes that generate landscape heterogeneity—like pyric herbivory—are probably more important for promoting biodiversity across all scales. Scale is a central problem in ecology, and defining scale in management objectives is essential for effective biodiversity conservation.</li> </ol>

Data for: Distribution of capitalized benefits from land conservation

Land conservation efforts throughout the U.S. enhance ecological amenities while generating wealth in the housing market through capitalization of amenities. This paper estimates the benefits of conservation that are capitalized into proximate home values and quantifies how those benefits are distributed across demographic groups. Using detailed property and household-level data from Massachusetts, we estimate that new land conservation led to $62 million in new housing wealth equity. However, houses owned by low-income or Black or Hispanic households are less likely to be located near protected areas, and hence, these populations are less likely to benefit financially. Direct study of the distribution of this new wealth from capitalized conservation is highly unequal, with the richest quartile of households receiving 43%, White households receiving 91%, and the richest White households receiving 40%, which is nearly 140% more than would be expected under equal distribution. We extend our analysis using census data for the entire United States and observe parallel patterns. We estimate that recent land conservation generated $9.8 billion in wealth through the housing market and that wealthier and White households benefited disproportionately. These findings suggest regressive and racially disparate incidence of the wealth benefits of land conservation policy.

Vulnerability of sea turtle nesting sites to erosion and inundation: a decision support framework to maximize conservation

Sandy beaches provide essential nesting habitat for sea turtles but are threatened globally by a rapidly changing climate. Identifying which nesting sites are at greatest risk from erosion and inundation remains an important goal of sea turtle conservation globally. Yet, efforts to identify at-risk sites have been hindered by the ability to model complex processes and incomplete information on nesting distribution and abundance. To assess the erosion and inundation risk to the reproductive success of a discrete genetic stock of flatback turtles (Natator depressus) across its nesting range in the Pilbara region of Western Australia, we used the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) Coastal Vulnerability Model. A relative exposure index was calculated for 402 nesting beaches in terms of six geophysical variables: wind and wave exposure, surge potential, relief, observed sea level rise and coastal geomorphology, and coupled with published information on the distribution and abundance of turtle tracks in the region. The majority of beaches (74%) had an intermediate to high exposure. In particular, 36% of beaches with a high abundance of flatback tracks (the top 25% of the frequency distribution) had a high exposure (the top 25% of the frequency distribution). This suggests that coastal exposure is a key vulnerability to the reproductive success of sea turtles that nest in this region. Promisingly, five beaches with a high abundance of turtle tracks also had a low exposure (bottom 25% of the frequency distribution) and these beaches may be critical for the long-term resilience of the stock against sea level rise and severe storms. Exposure varied across nesting sites and the approach presented here allows for a rapid and broadscale assessment of relative erosion and inundation risks at a scale most relevant to management.

opencc-zeroSep 2021View details →

FIG. 2 in Bryophytes from Glaziou's historical collections: revisiting the flora of Rio de Janeiro and implications for conservation

FIG. 2. — Species collected by Glaziou in the state of Rio de Janeiro.

opencc-by-4.0Apr 2023View details →

A dark side of conservation biology: protected areas fail in representing subterranean biodiversity. Databases.

We obtained distribution data for leiodids by digitizing the information provided by Fresneda and Salgado (2017). This information was updated and expanded with additional data from several sampling campaigns (unpublished data). For subterranean spiders, we included the entirety of the Alps range extending from France in the east westward through Switzerland, Italy, Liechtenstein, Austria, Germany, and Slovenia, by integrating available data in Global Biodiversity Information Facility (GBIF), Spider of Europe), Araneae.it  and other literature sources.

opencc-by-4.0Apr 2023View details →

Key files for: Comparative genomic analysis of Microcystis strain diversity using conserved marker genes

Key data outputs to accompany the manuscript "Comparative genomic analysis of Microcystis strain diversity using conserved marker genes"

Mitochondrial genome evolution in Annelida: A systematic study on conservative and variable gene orders and the factors influencing its evolution

The mitochondrial genomes of Bilateria are relatively conserved in their protein-coding, rRNA and tRNA gene complement, but the order of these genes can range from very conserved to very variable depending on the taxon. The supposedly conserved gene order of Annelida has been used to support the placement of some taxa within Annelida. Recently, authors have cast doubts on the conserved nature of the annelid gene order. Various factors may influence gene-order variability including, among others, increased substitution rates, base composition differences, structure of non-coding regions, parasitism, living in extreme habitats, short generation times and biomineralization. However, these analyses were neither done systematically, nor based on well-established reference trees. Several focused on only a few of these factors and biological factors were usually explored ad-hoc without rigorous testing or correlation analyses. Herein, we investigated the variability and evolution of the annelid gene order and the factors that potentially influenced its evolution, using a comprehensive and systematic approach. The analyses were based on 170 genomes, including 33 previously unrepresented species. Our analyses included 706 different molecular properties, 20 life-history and ecological traits and a reference tree corresponding to recent improvements concerning the annelid tree. The results showed that the gene order with and without tRNAs is generally conserved. However, individual taxa exhibit higher degrees of variability. None of the analyzed life-history and ecological traits explained the observed variability across mitochondrial gene orders. In contrast, the combination and interaction of the best predicting factors for substitution rate and base composition explained up to 30% of the observed variability. Accordingly, correlation analyses of different molecular properties of the mitochondrial genomes showed an intricate network of direct and indirect correlations between the different molecular factors. Hence, gene order evolution seems to be driven by molecular evolutionary aspects rather than by life history or ecology. On the other hand, gene order variability does not predict difficulty in placing certain taxa within molecular phylogenetic studies. We also discuss the molecular properties of annelid mitochondrial genomes considering canonical views on gene evolution and potential reasons why they do not always fit to the observed patterns without nuisance.

Genomic tools for comparative conservation genetics among three recently diverged stag beetles (Lucanus, Lucanidae)

We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedented rate of decline. However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remain challenging. We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex. We found that the three sky-island taxa formed three independently evolving units without detectable post-divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid-Pleistocene, have experienced episodes of demographic decline in the past. More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesized to impact the recent demographic history (< 100 years) differently, we found a shared pattern of continuous decline in effective population size among the three geographical taxa. We argue that future empirical studies should include more taxa, in addition to the focal species, that may or may not be affected by the focal historical events to avoid making biased conservation plans.