Overcoming confusion and stigma in habitat fragmentation research

Anthropogenic habitat loss is widely recognized as a primary environmental concern. By contrast, debates on the effects of habitat fragmentation persist. To facilitate overcoming these debates, here we: (i) review the state of the literature on habitat fragmentation, finding widespread confusion and stigma; (ii) identify consequences of this for biodiversity conservation and ecosystem management; and (iii) suggest ways in which research can move forward to resolve these problems. Confusion is evident from the 25 most-cited fragmentation articles published between 2017 and 2021. These articles use five distinct concepts of habitat fragmentation, only one of which clearly distinguishes habitat fragmentation from habitat area and other factors ('fragmentation per se'). Stigmatization is evident from our new findings that fragmentation papers are more charged with negative sentiments when compared to papers from other subfields in the environmental sciences, and that fragmentation papers with more negative sentiments are cited more. While most empirical studies of habitat fragmentation per se find neutral or positive effects on species and biodiversity outcomes, which implies that small habitat patches have a high cumulative value, confusion and stigma in reporting and discussing such results have led to suboptimal habitat protection policy. For example, government agencies, conservation organizations, and land trusts impose minimum habitat patch sizes on habitat protection. Given the high cumulative value of small patches, such policies mean that many opportunities for conservation are being missed. Our review highlights the importance of reducing confusion and stigma in habitat fragmentation research. To this end, we propose implementing study designs in which multiple sample landscapes are selected across independent gradients of habitat amount and fragmentation, measured as patch density. We show that such designs are possible for forest habitat across Earth's biomes. As such study designs are adopted, and as language becomes more precise, we expect that confusion and stigma in habitat fragmentation research will dissipate. We also expect important breakthroughs in understanding the situations where effects of habitat fragmentation per se are neutral, positive, or negative, and the reasons for these differences. Ultimately this will improve efficacy of area-based conservation policies, to the benefit of biodiversity and people.

Effects of Parental Care on the Magnitude of Inbreeding Depression: A Meta-Analysis in Fishes

AbstractInbreeding results from matings between relatives and often leads to a reduction in the fitness of inbred offspring, known as inbreeding depression. There is substantial variation in the magnitude of inbreeding depression among and within species, driven by differences in the biotic and abiotic environment. Recent studies in three species found that parental care has the potential to buffer against inbreeding depression in the offspring, but the generality of this pattern is still unknown. Here, we performed a meta-analysis to test whether variation in the magnitude of inbreeding depression is related to among-species differences in parental care in fishes. We synthesized 536 effect sizes across 56 studies and 18 species, spanning 47 years of research. We found that inbred offspring suffer a smaller reduction in fitness in species that provide biparental care than in species with uniparental or no care. By using a comparative approach, this study provides novel insights into the capacity of parental care to moderate inbreeding depression and suggests that these effects may currently be underappreciated. Considering the potential effects of parental care on inbreeding depression can help us understand why some species avoid inbreeding, whereas others tolerate or even prefer inbreeding, which has important implications for the maintenance of genetic variation within populations.

Conservation genetics of endangered Trillium govanianum Wall. ex D. Don - A pharmaceutically prized medicinal plant from the Himalaya and implications for species recovery

Understanding the genetic diversity and population structure of pharmaceutically important endangered plant species is crucial for their conservation and sustainable use. Despite the continuous population decline in Trillium govanianum Wall. ex D. Don, a highly prized medicinal plant endemic to the Himalaya, information regarding its conservation genetics has been lacking. Here, we employed a conservation genetics approach to investigate how drastically declining populations in natural habitats impact population genetic diversity and structure of this endangered species across the Kashmir Himalaya. We used Start codon targeted (SCoT) and Simple sequence repeat (SSR) markers to assess the intra- and inter-population genetic variation in seven sites across the study region. Based on these markers, we found a very low genetic diversity in T. govanianum populations. Very low levels of observed heterozygosity (Ho = 0.000) and that expected (He = 0.064) in the populations indicate high heterozygote deficiency and high levels of inbreeding depression (FIS = 1.000). A high genetic differentiation was observed among the populations for both SCoT (Gst = 0.719) and SSR (Fst = 0.707) markers. Both the markers showed low gene flow, SCoT (Nm = 0.195) and SSR (Nm = 0.119), depicting high among-population variation than within-population variation. Analysis of molecular variance also indicated a higher genetic variation between the populations than within populations. We also observed a significant positive correlation between genetic divergence and geographical distance, indicating that genetic differentiation in T. govanianum follows a pattern of isolation by distance. Bayesian structure and cluster analysis grouped the populations according to their geographical proximity. Further, redundancy analysis (RDA) revealed the presence of one polymorphic locus for each marker with high discriminatory power. Overall, our findings reveal a very low genetic diversity, high levels of inbreeding, and high genetic differentiation among the populations; likely resulting from habitat fragmentation, population isolation, bottleneck effect, low gene flow, and predominantly asexual reproduction currently operative in the species. Finally, based on the insights gained, we discuss the potential implications of our findings in guiding species recovery and habitat rehabilitation of T. govanianum in the Himalaya with conservation lessons for elsewhere in the world.

Genetic Structuring of One of the Main Vectors of Sylvatic Yellow Fever: Haemagogus (Conopostegus) leucocelaenus (Diptera: Culicidae)

Genetic diversity and population structuring for the species Haemogogus leucocelaenus, a sylvatic vector of yellow fever virus, were found to vary with the degree of agricultural land use and isolation of fragments of Atlantic Forest in municipalities in the state of São Paulo where specimens were collected. Genotyping of 115 mitochondrial SNPs showed that the populations with the highest indices of genetic diversity (polymorphic loci and mean pairwise differences between the sequences) are found in areas with high levels of agricultural land use (northeast of the State). Most populations exhibited statistically significant negative values for the Tajima D and Fu FS neutrality tests, suggesting recent expansion. The results show an association between genetic diversity in this species and the degree of agricultural land use in the sampled sites, as well as signs of population expansion of this species in most areas, particularly those with the highest forest edge densities. A clear association between population structuring and the distance between the sampled fragments (isolation by distance) was observed: samples from a large fragment of Atlantic Forest extending along the coast of the state of São Paulo exhibited greater similarity with each other than with populations in the northwest of the state.

Do habitat fragmentation and degradation influence the strength of fine-scale spatial genetic structure in plants? A global meta-analysis

As primarily sessile organisms, plants often show a non-random spatial distribution of genotypes over distance. This process known as fine-scale spatial genetic structure (FSGS) has been suggested through systematic reviews to depend on life form, mating system, and pollen and seed dispersal vectors, while there is no consensus on its behaviour due to external factors, such as anthropogenic habitat changes. By conducting a systematic review and global meta-analysis of empirical FSGS studies, we aimed to evaluate how anthropogenic habitat fragmentation and degradation influence the strength of FSGS in plant populations by means of the Sp statistic. Moreover, we tested how pollination and seed dispersal vectors contribute to the variation of the Sp statistic. We retrieved 243 FSGS studies from 1960 to 2020 of which only 65 were informative for the systematic review. Most empirical studies comprised outcrossers (84%) and trees (67%), with few herbs (23%) and scarce annual species (2%). In weighted meta-analyses for 116 plant populations (31 studies), we did not detect significant effects in the magnitude of effect sizes for the Sp statistic among undisturbed, degraded and fragmented habitats. Results showed significant effects for seed dispersal vectors, but not for pollination. Overall, we observed high variation among the effect sizes (not related to the goodness-of-fit of mixed models) of habitat status, pollination and seed dispersal categories, which precludes identifying biological trends on the Sp statistic. More empirical studies are needed that contrast multiple plant populations in disturbed versus undisturbed habitats, and by increasing the taxonomic groups, such as herbs and annual plants.

Are There Edge Effects on the Genetic Diversity of the Trap-Jaw Ant Odontomachus chelifer (Formicidae: Ponerinae) in a Neotropical Savanna Fragment? A First Assessment

Habitat fragmentation is considered an important threat to biodiversity, increasing species exposure to edge effects. The Brazilian Cerrado savanna is considered a biodiversity hotspot and has been converted to small, isolated fragments due to human activities. Ant communities and colony survivorship are known to be affected by edge effects in Cerrado, but to date there is no information on the genetic diversity of ant colonies at the edge of fragmented areas. Here, we investigate if colony genetic diversity and structure of Odontomachus chelifer (Latreille) ants (Hymenoptera: Formicidae) are subject to edge effects in a Cerrado reserve in southeast Brazil. Using microsatellites, we evaluated the number of breeders (queens and males) and the genetic diversity in O. chelifer colonies located in the interior versus edge of a Cerrado fragment. All O. chelifer nests had multiple queens, which presented a low mating frequency. The number of breeders and most estimates of genetic diversity did not differ between colonies at the edge versus interior of the fragment. Genetic structure was not influenced by nest location as well. However, we detected a small and positive increase in the observed heterozygosity in colonies located at fragment edges. High heterozygosity is thought to be particularly important in fast-changing environments, such as edges, providing an advantage for genetic diversity. Further investigation is needed to assess in greater detail how habitat loss affects O. chelifer biology. Our study is a first step toward elucidating edge effects on genetic diversity of ant colonies, a topic still poorly explored in tropical environments.

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 the 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.

The impact of habitat loss on molecular signatures of coevolution between an iconic butterfly (Alcon blue) and its host plant (Marsh gentian)

Habitat loss is threatening natural communities worldwide. Small and isolated populations suffer from inbreeding and genetic drift, which jeopardize their long-term survival and adaptive capacities. However, the consequences of habitat loss for reciprocal coevolutionary interactions remain poorly studied. In this study, we investigated the effects of decreasing habitat patch size and connectivity associated with habitat loss on molecular signatures of coevolution in the Alcon blue butterfly (Phengaris alcon) and its most limited host, the marsh gentian (Gentiana pneumonanthe). Because reciprocal coevolution is characterized by negative frequency-dependent selection as a particular type of balancing selection, we investigated how signatures of balancing selection vary along a gradient of patch size and connectivity, using single nucleotide polymorphisms (SNPs). We found that signatures of coevolution were unaffected by patch characteristics in the host plants. On the other hand, more pronounced signatures of coevolution were observed in both spatially isolated and in large Alcon populations, together with pronounced spatial variation in SNPs that are putatively involved in coevolution. These findings suggest that habitat loss can facilitate coevolution in large butterfly populations through limiting swamping of locally beneficial alleles by maladaptive ones. We also found that allelic richness (Ar) of the coevolutionary SNPs is decoupled from neutral Ar in the butterfly, indicating that habitat loss has different effects on coevolutionary as compared with neutral processes. We conclude that this specialized coevolutionary system requires particular conservation interventions aiming at generating a spatial mosaic of both connected and of isolated habitat to maintain coevolutionary dynamics.

Evaluating the genetic consequences of population subdivision as it unfolds and how to best mitigate them: A rare story about koalas

The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12% and 69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.

The Grassland Fragmentation Experiment in the Swiss Jura Mountains: A Synthesis

We synthesize findings from a 7-year fragmentation experiment in species-rich, nutrient-poor, dry calcareous grasslands in the north-western Jura mountains, Switzerland. We used a standardized approach with 48 fragments (0.25–20.25 m2) and corresponding control plots in three sites. The 5-m-wide isolation area around the fragments was maintained by frequent mowing. Fragments experienced various ecological changes, e.g., plant biomass increased along fragment edges. We examined fragmentation effects on species richness and composition, abundance, genetic diversity, functional diversity, species traits and species interactions (pollination, herbivory, parasitism, disease) in a wide array of invertebrate (gastropods, spiders, woodlice, various insect groups) and plant taxa. Responses to fragmentation differed between taxonomical groups and species. While species richness and individual density were lower in fragments in some groups, the opposite was true for other groups. Fragmentation effects were most pronounced on species interactions; however, some effects only occurred with a delay. For example, fragmentation influenced foraging patterns of bumblebees, affecting pollination, which in turn resulted in a decreased outcrossing frequency and reduced genetic diversity in a focal plant species. We highlight key findings of the experiment and emphasize their implications for grassland conservation.

Genetic Diversity, Conservation, and Utilization of Plant Genetic Resources

Plant genetic resources (PGRs) are the total hereditary material, which includes all the alleles of various genes, present in a crop species and its wild relatives. They are a major resource that humans depend on to increase farming resilience and profit. Hence, the demand for genetic resources will increase as the world population increases. There is a need to conserve and maintain the genetic diversity of these valuable resources for sustainable food security. Due to environmental changes and genetic erosion, some valuable genetic resources have already become extinct. The landraces, wild relatives, wild species, genetic stock, advanced breeding material, and modern varieties are some of the important plant genetic resources. These diverse resources have contributed to maintaining sustainable biodiversity. New crop varieties with desirable traits have been developed using these resources. Novel genes/alleles linked to the trait of interest are transferred into the commercially cultivated varieties using biotechnological tools. Diversity should be maintained as a genetic resource for the sustainable development of new crop varieties. Additionally, advances in biotechnological tools, such as next-generation sequencing, molecular markers, in vitro culture technology, cryopreservation, and gene banks, help in the precise characterization and conservation of rare and endangered species. Genomic tools help in the identification of quantitative trait loci (QTLs) and novel genes in plants that can be transferred through marker-assisted selection and marker-assisted backcrossing breeding approaches. This article focuses on the recent development in maintaining the diversity of genetic resources, their conservation, and their sustainable utilization to secure global food security.

Characterization of the Genetic Variability within Ziziphus nummularia Genotypes by Phenotypic Traits and SSR Markers with Special Reference to Geographic Distribution

Understanding the impacts and constraints of climate change on Ziziphus nummularia's geographical distribution is crucial for its future sustainability. In this study, we analyze information obtained from the field investigation, the distribution and response of climatic changes of Ziziphus nummularia by the use of ArcGIS analysis. The genetic diversity of 180 genotypes from three populations was studied by morphological attributes and simple sequence repeat (SSR). The results showed that the significant bioclimatic variable limiting the distribution of Z. nummularia was the mean temperature (bio 10_18.tif and bio19). Under the current climatic change, the suitable growth region of Z. nummularia is Swat (35.22° N, 72.42° E), while the future distribution would be Buner (34.39° N, 72.61° E), respectively. A total of 11 phenotypic traits were noted and had significant phenotypic variation among the traits. A total of 120 alleles were amplified. The alleles per locus ranged from 2 to 6, averaging 4.42, whereas PIC ranged from 0.33 to 0.79. Within a mean value of 0.67 per locus, expected heterozygosity was 0.57, observed heterozygosity was 0.661, and average gene diversity was 0.49. Flow estimates (6.41) indicated frequent gene flow within genotypes. The clustering, STRUCTURE, and PCoA analysis indicated Swat and Buner migration routes and evolution as well. The results indicated the prevalence of genetic variability and relationships among Z. nummularia across geographical boundaries had retained unique alleles. This may facilitate the development of agronomically desirable cultivars. However, climate change has impacted species distributions, requiring strategies to conserve genetic resources in different areas.

Micropropagation of berry crops for creation of germplasm cryobanks

One of the main stages of cryopreservation of meristematic tissues in vegetative plants is a clonal micropropagation, which includes isolating the explants of the raw material in vitro and optimizing the culture medium for micropropagation. As the result of our studies, the optimal periods for in vitro micropropagation are: first - isolation of explants from initiated shoots of dormant buds (blackcurrants and raspberries) in January-March; the second - from actively growing shoots (blackcurrants and raspberries) in May-June, from the formed mustache (strawberry) in July-August. The optimal drugs for sterilization of raspberry explants are: a) 0.1% HgCl2 (6 min), then 3% H2O2 (15 min); b) chlorine-containing bleach «Domestos» in the dilution of H2O 1:9 (10 min). For blackcurrant: a) 0.1% HgCl2 (5 min) in combination with 0.1% fungicide "Topaz" (30 min); b) 0.1% HgCl2 (5 min) in combination with the treatment with KMnO4 (30 min); c) "Domestos" in the dilution of H2O 1:5 (20 min). For strawberry: a) 0.1% HgCl2 (6 min) followed by treatment with 3% H2O2 10 (min); b) 1% deochlor (7 min), 3% H2O2 (10 min); c) "Domestos" in the dilution of H2O 1:5 (8 min) with subsequent treatment 0,1% HgCl2 -7 min, then 0,20 mg/l КМnO4 - 30 min. Optimal compositions of culture media for micropropagation of blackcurrant - Murashige and Skoog (MS) medium with 0.5 mg L-1 BAP, 0.5 mg L-1 GA3, 0.1 mg L-1 IBA and 20 g L-1 glucose. For raspberry -MS medium with 0.5 mg L-1 BAP, 0.1 mg L-1 IBA, 10 mg L-1 iron chelate and 30 g L-1 sucrose. For strawberry - MS medium with 0.3 mg L-1 BAP, 0.01 mg L-1 IBA, 0.2 mg L-1 GA3, 10 mg L-1 iron chelate and 30 g L-1 sucrose. Based on these studies, the cryobank was created, which include the germplasm of in vitro meristematic tissues in 66 cultivars, hybrids and wild-growing forms of blackcurrant, raspberry and strawberry. Therefore, the aim of the research was to obtain aseptic plants, clonal micropropagation and the creation of a cryogenic collection of germplasm based on the developed technology.

From poops to planning: A broad non-invasive genetic survey of large mammals from the Indian Himalayan Region

Large forested landscapes often harbour significant amount of biodiversity and support mankind by rendering various livelihood opportunities and ecosystem services. Their periodic assessment for health and ecological integrity is essential for timely mitigation of any negative impact of human use due to over harvesting of natural resources or unsustainable developmental activities. In this context, monitoring of mega fauna may provide reasonable insights about the connectivity and quality of forested habitats. In the present study, we conducted a largest non-invasive genetic survey to explore mammalian diversity and genetically characterized 13 mammals from the Indian Himalayan Region (IHR). We analyzed 4806 faecal samples using 103 autosomal microsatellites and with three mitochondrial genes, we identified 37 species of mammal. We observed low to moderate level of genetic variability and most species exhibited stable demographic history. We estimated an unbiased population genetic account (PGA_unbias) for 13 species that may be monitored after a fixed time interval to understand species performance in response to the landscape changes. The present study has been evident to show pragmatic permeability with the representative sampling in the IHR in order to facilitate the development of species-oriented conservation and management programmes.

Recent Changes in Genetic Diversity, Structure, and Gene Flow in a Passerine Experiencing a Rapid Population Decline, the Dupont’s Lark (Chersophilus duponti)

Monitoring temporal dynamics in genetic diversity is of great importance for conservation, especially for threatened species that are suffering a rapid population decline and increased fragmentation. Here, we investigate temporal variation in genetic diversity, structure, and gene flow in the Dupont’s lark (Chersophilus duponti) across most of its range. This species shows increasing levels of population fragmentation, substantial population declines, and severe range contraction, so temporal losses of genetic diversity, increasing differentiation, and decreasing gene flow are expected when comparing present day data with previous situations. To address this, we resampled sites (nine regions in two countries) after 12–15 years (five-to-seven generations) and assessed changes in genetic parameters using 11 microsatellite markers. We found no substantial loss in genetic diversity over time at the species level, but we detected considerable variation among regions in the amount of allelic diversity and heterozygosity lost over time. Temporal variation in allele frequencies (common, rare, and private alleles), and changes in genetic differentiation and gene flow over time suggest a major role of connectivity for the stability of the overall metapopulation. Our results agree with the hypothesis that connectivity rescues genetic diversity via immigration and gene flow. However, evidence of recent genetic bottleneck and the substantial changes detected in some regions are clear signs of genetic erosion and may be signalling a rapid decline of the populations. Urgent actions must be carried out to stop and reverse human impacts on this threatened lark and its habitat.

Contrasting Responses of Alien and Ancient Forest Indicator Plant Species to Fragmentation Process in the Temperate Lowland Forests

Fragmentation is one of the major threats to biodiversity. In a fragmented landscape, forest specialists are losing suitable forest habitats with specific site and microclimate conditions, which results in their local extinction. Conversely, the invasion of alien species is facilitated by open forest areas and increased boundaries between forest fragments and adjacent land. We studied the effect of fragmentation in terms of fragment size impact on overall plant species richness and on selected ecologically important groups' richness, composition, and diversity. We surveyed vegetation in the interior of 47 fragments of various sizes and one unfragmented reference forest. Our results reveal that the effect of fragmentation is complex and differs for studied plant groups. Decreasing fragment size negatively affects the overall plant richness and richness of native and ancient forest indicator plants as well as their diversity, while the effect is positive for alien plants. The highest proportion of ancient forest indicator plant species and the lowest proportion of alien plants in the unfragmented forest underline the great conservation value of forest fragments. At the same time, our results reveal that large and diverse forest ecosystems are susceptible to biological invasions as well.

Population structure and genetic variation of fragmented mountain birch forests in Iceland

Betula pubescens Ehrh. (mountain birch) is the only forest-forming tree in Iceland. Since human settlement (874 AD), the continuous 25,000-30,000 km 2 forest has shrunk to 1.200 km 2 of fragmented patches, making it a good object to study population genetic consequences of habitat fragmentation and disturbance. Further, genetic studies have also shown that hybridization between the tetraploid (2n=56) B. pubescens and the diploid (2n=28) Betula nana L. (dwarf birch) occurs among Iceland's natural populations. This study assessed the genetic variation within and among eleven birch forests remaining across Iceland. Genotype-by-sequencing methodology (GBS) provided a total of 24,585 SNPs, with a minor allele frequency > 5% for genetic analyses. The analysis showed similar diversity within forests, suggesting that fragmentation and hybridization have had a limited effect on the genetic variation within sites. A clear genetic divergence is found among forests from the different regions of Iceland that may reflect historical isolation; the differentiation between forests increased with geographic distances reflecting isolation by distance. Information on the distribution of genetic variation of birch in Iceland is essential for its conservation and to establish genotype-phenotype associations to predict responses to new environmental conditions imposed by climate change and novel biotic/abiotic stressors.

Landscape genetics of a sub-alpine toad: climate change predicted to induce upward range shifts via asymmetrical migration corridors

Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the twenty-first century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations, yet our understanding of climatic influences on population connectivity is limited. In this study, we used a previously published double-digest RADseq dataset along with numerous remotely sensed habitat features in a landscape genetics framework to answer two primary questions in Yosemite National Park: (1) Which fine-scale climate, topographic, soil, and vegetation features most facilitate meadow connectivity? (2) How is climate change predicted to influence both the magnitude and net asymmetry of genetic migration? We developed an approach for simultaneously modeling multiple toad migration paths, akin to circuit theory, except raw environmental features can be separately considered. Our workflow identified the most likely migration corridors between meadows and used the unique cubist machine learning approach to fit and forecast environmental models of connectivity. We identified the permuted modeling importance of numerous snowpack-related features, such as runoff and groundwater recharge. Our results highlight the importance of considering phylogeographic structure, and asymmetrical migration in landscape genetics. We predict an upward elevational shift for this already high-elevation species, as measured by the net vector of anticipated genetic movement, and a north-eastward shift in species distribution via the network of genetic migration corridors across the park.

Antelope space‐use and behavior indicate multilevel responses to varying anthropogenic influences in a highly human‐dominated landscape

A primary means of conserving a species or a habitat in a human‐dominated landscape is through promoting coexistence with humans while minimizing conflict. For this, we should understand how wildlife is impacted by direct and indirect human activities. Such information is rare in areas with high human densities. To investigate how animals respond to altered ecological conditions in human‐dominated landscapes, we focused on a wild herbivore of conservation concern in the Krishnasaar Conservation Area (KrCA) in Nepal. Here, blackbuck Antilope cervicapra, a generalist grazer, lives in refugia located with a growing human population. We studied the impacts of humans on habitat use and behavior of blackbuck. We laid 250 × 250 m grid cells in the entire KrCA and carried out indirect sign surveys with three replications for habitat use assessment. We observed herds of blackbuck for 89 h in different habitat types using scan sampling methods. Our habitat‐use survey showed that habitats under intensive human use were hardly used by blackbuck, even when high‐quality forage was available. Habitat openness was the major predictor of habitat use inside the core area, where levels of human activities were low. We also found a positive correlation between habitat use by blackbuck and livestock. Blackbuck were substantially more vigilant when they were in forest than in grassland, again indicating an influence of risk. Overall, blackbuck appear to be sensitive to the risk associated with both natural and anthropogenic factors. Our findings have direct implications for managing human–wildlife interactions in this landscape, specifically regarding strategies for livestock grazing in habitats highly used by blackbuck and concerning predictions of how changing land use will impact the long‐term persistence of blackbuck. Our work suggests that wild herbivores may be able to persist in landscapes with high human densities so long as there are refuges where human activities are relatively low.

Challenges in quantifying genome erosion for conservation

Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.

Genetic diversity and differentiation of populations of Anthyllis vulneraria along elevational and latitudinal gradients

The abundant centre model (ACM) predicts that the suitability of environmental conditions for a species decreases from the centre of its distribution toward its range periphery and, consequently, its populations will become scarcer, smaller and more isolated, resulting in lower genetic diversity and increased differentiation. However, little is known about whether genetic diversity shows similar patterns along elevational and latitudinal gradients with similar changes in important environmental conditions. Using microsatellite markers, we studied the genetic diversity and structure of 20 populations each of Anthyllis vulneraria along elevational gradients in the Alps from the valleys to the elevational limit (2500 m) and along a latitudinal gradient (2500 km) from Central Europe to the range margin in northern Scandinavia. Both types of gradients corresponded to an 11.5°C difference in mean annual temperature. Genetic diversity strongly declined and differentiation increased with latitude in line with the predictions of the ACM. However, as population size did not decline with latitude and genetic diversity was not related to population size in A. vulneraria, this pattern is not likely to be due to less favorable conditions in the North, but due to serial founder effects during the post‐glacial recolonization process. Genetic diversity was not related to elevation, but we found significant isolation by distance along both gradients, although the elevational gradient was shorter by orders of magnitude. Subarctic populations differed genetically from alpine populations indicating that the northern populations did not originate from high elevational Alpine ones. Our results support the notion that postglacial latitudinal colonization over large distances resulted in a larger loss of genetic diversity than elevational range shifts. The lack of genetic diversity in subarctic populations may threaten their long‐term persistence in the face of climate change, whereas alpine populations could benefit from gene flow from low‐elevation populations.

Coping With Dynamism: Phylogenetics and Phylogeographic Analyses Reveal Cryptic Diversity in Heleobia Snails of Atacama Saltpan, Chile

The species that inhabit systems highly affected by anthropic activities usually exhibit this external influence in their gene pool. In this study, we investigated the genetic patterns of populations of Heleobia atacamensis, a freshwater microgastropod endemic to the Atacama Saltpan, a system historically exposed to environmental changes, and currently subjected to conditions associated with metallic and non-metallic mining and other anthropic activities. Molecular analyses based on nuclear and mitochondrial sequences indicate that the saltpan populations are highly fragmented and that the genetic structure is mainly explained by historical geographic isolation, with little influence of contemporary factors. The microsatellite results suggest a moderate genetic diversity and sharp differentiation mediated by isolation by distance. Additionally, despite the high environmental heterogeneity detected and the marked historical dynamism of the region, our data reveal no signs of demographic instability. The patterns of contemporary gene flow suggest a change in the current genetic structure, based on the geographic proximity and specific environmental conditions for each population. Our results, highlight the role of fragmentation as a modulator of genetic diversity, but also suggest that the historical persistence of isolated populations in naturally dynamic environments could explain the apparent demographic stability detected.

A greater yellowstone ecosystem grizzly bear case study: genetic reassessment for managers

There are five grizzly bear (Ursus arctos horribilis) populations in the lower 48 states of the United States. My goal in this Commentary was to ascertain whether genetic diversity is being lost from the isolated GYE grizzly bear population and to better understand any viability implications. I reviewed the scientific literature, including two key genetic studies that the US Fish and Wildlife Service (USFWS) relied upon for their 2007 and current 2017 GYE grizzly bear genetics policy. I discovered that some studies reveal a loss of heterozygosity in the GYE bear population, both historically and in recent decades. Some had a statistically significant depletion rate. My review took place periodically between 2010 and 2021 and indicates that the genome of the GYE grizzly bear population is too small for long-term adaptation. The paper includes a discussion about evolutionary adaptation which invokes time frames rarely considered by nature conservation planners. I also examined genetic statements in the USFWS’s 2017 GYE grizzly bear delisting regulations and highlighted those that seem incongruent with current scientific thought. If this paper is read by some scientists, land managers, administrators, environmentalists, and others with some genetics background, they will better understand some USFWS decisions and policy statements. This case study illustrates that land management agencies can provide a one-sided treatment of some science when writing regulations about genetics.

Climate Change Impacts and Extinction Risk Assessment of Nepeta Representatives (Lamiaceae) in Greece

The ongoing climate change has already left its imprint on species distributions, with rare, endemic species being more threatened. These changes are more prominent in regional biodiversity hotspots, such as Greece, which is already facing the short term impacts of human induced climate change. Greek flora hosts numerous endemic medicinal and aromatic plant taxa (MAPs), which are economically important and provide integral ecosystem services. The genus Nepeta is one of the largest Lamiaceae genera, containing several MAPs, yet, despite its taxonomical and economical significance, it remains vastly understudied in Greece. We explore the effects of climate change on the range of the Greek endemic Nepeta MAPs, via a species distribution models (SDMs) approach in an ensemble modeling framework, using soil, topographical and bioclimatic variables as predictors in three different time steps. By doing so, we attempt to estimate the current and future extinction risk of these taxa and to locate their current and future species richness hotspots in Greece. The taxa analyzed are expected to experience severe range retractions, with minor intraspecific variation across all time steps (p > 0.05), driven mainly by soil- and aridity-related variables. The extinction risk status of only one taxon is predicted to worsen in the future, while all other taxa will remain threatened. Current species richness hotspots are mainly located in southern Greece and are projected to shift both altitudinally and latitudinally over time (p < 0.01).

Response of Iranian lizards to future climate change by poleward expansion, southern contraction, and elevation shifts

This study explores the relationships between recent Iranian lizard species distributions and the observed climate, as well as potential future distributions of species. For this purpose, an ensemble of seven algorithms was used to forecast the distributions of 30 species for the recent and future (2070) based on the averages of 14 global climate models under optimistic (RCP2.6) and pessimistic (RCP8.5) scenarios. Annual precipitation (n = 16) and annual mean temperature (n = 7) were identified as the most important variables in determining the distribution of 76.66% (23 out of 30) of the species. The consensus model predicts that the ranges of 83.33% of species (n = 25) have the potential to expand poleward at higher latitudes while preserving the majority of their recent distributions (except for four species). Furthermore, the ranges of the remaining species (n = 5) will be preserved at higher latitudes. However, they (n = 22) may contract slightly (n = 13) or excessively (n = 9) in the south of their distribution range at lower latitudes. These results indicate that species (N = 19) situated in mountainous areas such as the Zagros, Alborz, and Kopet Dagh may move or maintain their range at higher elevations as a result of future climate change. Finally, this study suggests that 30% of species (n = 9) may be threatened by future climate change and that they should be prioritized in conservation efforts.

Recapitulating whole genome based population genetic structure for Indian wild tigers through an ancestry informative marker panel

Identification of genetic structure within wildlife populations have implications in their conservation and management. Accurately inferring population genetic structure requires whole-genome data across the geographical range of the species, which can be resource-intensive. A cheaper strategy is to employ a subset of markers that can efficiently recapitulate the population genetic structure inferred by the whole genome data. Such ancestry informative markers (AIMs), have rarely been developed for endangered species such as tigers utilizing single nucleotide polymorphisms (SNPs). Here, we first identify the population structure of the Indian tiger using whole-genome sequences and then develop an AIMs panel with a minimum number of SNPs that can recapitulate this structure. We identified four population clusters of Indian tigers with North-East, North-West, and South Indian tigers forming three separate groups, and Terai and Central Indian tigers forming a single cluster. To evaluate the robustness of our AIMs, we applied it to a separate dataset of tigers from across India. Out of 92 SNPs present in our AIMs panel, 49 were present in the new dataset. These 49 SNPs were sufficient to recapitulate the population genetic structure obtained from the whole genome data. To the best of our knowledge, this is the first-ever SNP-based AIMs panel for big cats, which can be used as a cost-effective alternative to whole-genome sequencing for detecting the biogeographical origin of Indian tigers. Our study can be used as a guideline for developing an AIMs panel for the management of other endangered species where obtaining whole genome sequences are difficult.

Comparing the population structure of the specialist Butler’s Gartersnake (Thamnophis butleri) and the generalist Eastern Gartersnake (Thamnophis sirtalis sirtalis) in Ontario (Canada) and Michigan (USA)

Species differing in life-history attributes vary in their responses to features within a shared landscape. We evaluated genetic structure of sympatric gartersnake species in southwestern Ontario (Canada) and southeastern Michigan (USA), where habitat fragmentation is high due to agriculture and urbanization. We surveyed genetic structure of a habitat specialist, Butler’s Gartersnake (Thamnophis butleri (Cope, 1889)), and a habitat generalist, Eastern Gartersnake (Thamnophis sirtalis sirtalis (Linnaeus, 1758)), using DNA microsatellites. Bayesian clustering, discriminant analysis of principal components, and pairwise population comparisons revealed genetic differentiation among three major regional clusters of Butler’s Gartersnake with evidence of further division within one. Genetic clustering of Butler’s Gartersnake suggest that inhospitable habitat limits dispersal. Eastern Gartersnakes showed less structure, with assignment tests implying a single genetic cluster. We found positive significant Mantel’s r for both species in the smallest distance class (<15 km), but significant isolation by distance for Butler’s Gartersnake only. These findings together imply that connectivity for Eastern Gartersnakes is less impacted by habitat loss and fragmentation or that we were less able to detect their effects. Our study shows the value of multispecies comparisons in studies seeking to understand the underlying causes of genetic structure in natural populations.

Anthropogenic fragmentation increases risk of genetic decline in the threatened orchid Platanthera leucophaea

Protecting biodiversity requires an understanding of how anthropogenic changes impact the genetic processes associated with extinction risk. Studies of the genetic changes due to anthropogenic fragmentation have revealed conflicting results. This is likely due to the difficulty in isolating habitat loss and fragmentation, which can have opposing impacts on genetic parameters. The well-studied orchid, Platanthera leucophaea, provides a rich dataset to address this issue, allowing us to examine range-wide genetic changes. Midwestern and Northeastern United States. We sampled 35 populations of P. leucophaea that spanned the species' range and varied in patch composition, degree of patch isolation, and population size. From these populations we measured genetic parameters associated with increased extinction risk. Using this combined dataset, we modeled landscape variables and population metrics against genetic parameters to determine the best predictors of increased extinction risk. All genetic parameters were strongly associated with population size, while development and patch isolation showed an association with genetic diversity and genetic structure. Genetic diversity was lowest in populations with small census sizes, greater urbanization pressures (habitat loss), and small patch area. All populations showed moderate levels of inbreeding, regardless of size. Contrary to expectation, we found that critically small populations had negative inbreeding values, indicating non-random mating not typically observed in wild populations, which we attribute to selection for less inbred individuals. The once widespread orchid, Platanthera leucophaea, has suffered drastic declines and extant populations show changes in the genetic parameters associated with increased extinction risk, especially smaller populations. Due to the important correlation with risk and habitat loss, we advocate continued monitoring of population sizes by resource managers, while the critically small populations may need additional management to reverse genetic declines.

Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures

Genome sequencing of spatially distributed individuals sheds light on how evolution structures genetic variation. Populations of Phellopilus nigrolimitatus, a red-listed wood-inhabiting fungus associated with old-growth coniferous forests, have decreased in size over the last century due to a loss of suitable habitats. We assessed the population genetic structure and investigated local adaptation in P. nigrolimitatus, by establishing a reference genome and genotyping 327 individuals sampled from 24 locations in Northern Europe by RAD sequencing. We revealed a shallow population genetic structure, indicating large historical population sizes and high levels of gene flow. Despite this weak sub-structuring, two genetic groups were recognized; a western group distributed mostly in Norway and an eastern group covering most of Finland, Poland and Russia. This sub-structuring may reflect co-immigration with the main host, Norway spruce (Picea abies), into Northern Europe after the last ice age. We found evidence of low levels of genetic diversity in southwestern Finland, which has a long history of intensive forestry and urbanization. Numerous loci were significantly associated with one or more environmental factors, indicating adaptation to specific environments. These loci clustered into two groups with different associations with temperature and precipitation. Overall, our findings indicate that the current population genetic structure of P. nigrolimitatus results from a combination of gene flow, genetic drift and selection. The acquisition of similar knowledge especially over broad geographic scales, linking signatures of adaptive genetic variation to evolutionary processes and environmental variation, for other fungal species will undoubtedly be useful for assessment of the combined effects of habitat fragmentation and climate change on fungi strongly bound to old-growth forests.

Gene Flow and Genetic Structure Reveal Reduced Diversity between Generations of a Tropical Tree, Manilkara multifida Penn., in Atlantic Forest Fragments

The Atlantic Forest remnants in southern Bahia, Brazil, contain large tree species that have suffered disturbances in recent decades. Anthropogenic activities have led to a decrease in the population of many tree species and a loss of alleles that can maintain the evolutionary fitness of their populations. This study assessed patterns of genetic diversity, spatial genetic structure, and genetic structure among Manilkara multifida Penn. populations, comparing the genetic parameters of adult and juvenile trees. In particular, we collected leaves from adults and juveniles of M. multifida in two protected areas, the Veracel Station (EVC) and the Una Biological Reserve (UBR), located in threatened Atlantic Forest fragments. We observed a substantial decay in genetic variability between generations in both areas i.e., adults’ H_O values were higher (EVC = 0.720, UBR = 0.736) than juveniles’ (EVC = 0.463 and UBR = 0.560). Both juveniles and adults showed genetic structure between the two areas (θ = 0.017 for adults and θ = 0.109 for juveniles). Additionally, forest fragments indicated an unexpectedly short gene flow. Our results, therefore, highlight the pervasive effects of historical deforestation and other human disturbances on the genetic diversity of M. multifida populations within a key conservation region of the Atlantic Forest biodiversity hotspot.

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (F _ROH = 0.57) than the large-connected (F _ROH = 0.35 and F _ROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.

Development and utilization of microsatellite markers to assess genetic variation coupled with modelling range shifts of Dodonaea viscosa (L.) Jacq. in isolated Taita Hills and Mount Kenya forests

BACKGROUND

Understanding genetic variation is critical for the protection and maintenance of fragmented and highly disturbed habitats. The Taita Hills of Kenya are the northernmost part of the Eastern Arc Mountains and have been identified as one of the world's top ten biodiversity hotspots. Over the past century the current forests in the Taita Hills have become highly fragmented. In order to appraise the influence of anthropological disturbance and fragmentation on plant species in these mountains, we studied the genetic variation and population structure of Dodonaea viscosa (L.) Jacq. (Sapindaceae), using newly developed microsatellite (SSR) markers, combined with ecological niche modelling analyses (ENMs).

METHODS AND RESULTS

We utilized the Illumina paired-end technology to sequence D. viscosa's genome and developed its microsatellite markers. In total, 646,428 sequences were analyzed, and 49,836 SSRs were identified from 42,638 sequences. A total of 18 out of 25 randomly selected primer pairs were designed to test polymorphism among 92 individuals across eight populations. The average observed heterozygosity and expected heterozygosity ranged from 0.119 to 0.982 and from 0.227 to 0.691, respectively. Analysis of molecular variance (AMOVA) revealed 78% variance within populations and only 20% among the eight populations. According to ENM results, D. viscosa's suitable habitats have been gradually reducing since the last glacial maximum (LGM), and the situation will worsen under the extreme pessimist scenario of (representative concentration pathway) RCP 8.5. Moreover, genetic diversity was significantly greater in larger fragments.

CONCLUSIONS

In the present study, we successfully developed and tested SSR markers for D. viscosa. Study results indicate that fragmentation would constitute a severe threat to plant forest species. Therefore, urgent conservation management of smaller fragmented patches is necessary to protect this disturbed region and maintain the genetic resources.

Strong sexual selection fails to protect against inbreeding-driven extinction in a moth

Sexual selection is predicted to influence population persistence because skew in male reproductive success may facilitate the purging of mutation load. We manipulated the strength of sexual selection in populations of Indian meal moths, Plodia interpunctella, by adjusting adult sex ratios to be either male- or female-biased, leading to strong and weak sexual selection in males, respectively. After between 19 and 22 generations of experimental evolution, we examined whether mutation load differed between these populations by enforcing successive generations of inbreeding, tracking extinction events, offspring viability and assaying the effect of inbreeding on male mating success and female choice. We found no effect of the strength of sexual selection on the rate of extinction or offspring viability. We did, however, find changes in both male mating success and female choice, with both being influenced by the sex ratio treatment and the number of generations of inbreeding. Males from male-biased populations were more successful at mating with stock females, and mating success declined rapidly with inbreeding regardless of sex ratio treatment. Females from male-biased populations were less likely to mate with stock males at the onset of the experiment, but tended to mate more frequently with increasing inbreeding compared to females from female-biased populations. Our results demonstrate that while mating behaviors have diverged between male-biased and female-biased lines mutation loads remained similar. This suggests that the benefits of sexual selection to population fitness may be low or slow to accumulate under the benign environmental conditions in which these populations evolved.

Opportunities and challenges of macrogenetic studies

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

Moderate Genetic Diversity and Demographic Reduction in the Threatened Giant Anteater, Myrmecophaga tridactyla

In general, large mammal species with highly specialized feeding behavior and solitary habits are expected to suffer genetic consequences from habitat loss and fragmentation. To test this hypothesis, we analyzed the genetic diversity distribution of the threatened giant anteater inhabiting a human-modified landscape. We used 10 microsatellite loci to assess the genetic diversity and population structure of 107 giant anteaters sampled in the Brazilian Central-Western region. No genetic population structuring was observed in this region suggesting no gene flow restriction within the studied area. On the other hand, the moderate level of genetic diversity (Ho = 0.54), recent bottleneck detected and inbreeding (F_is, 0.13; p ≤ 0.001) signatures suggest potential impacts on the genetic variation of this Xenarthra. Additionally, a previous demographic reduction was suggested. Thus, considering the increased human-promoted impacts across the entire area of distribution of the giant anteater, our results can illustrate the potential effects of these disturbances on the genetic variation, allowing us to request the long-term conservation of this emblematic species.

Do all roads lead to resistance? State road density is the main impediment to gene flow in a flagship species inhabiting a severely fragmented anthropogenic landscape

AIM

Connectivity conservation is ideally based on empirical information on how landscape heterogeneity influences species-specific movement and gene flow. Here, we present the first large-scale evaluation of landscape impacts on genetic connectivity in the European wildcat (Felis silvestris), a flagship and umbrella species for connectivity conservation across Europe.

LOCATION

The study was carried out in the core area of the distributional range of wildcats in Germany, covering about 186,000 km2 of a densely populated and highly fragmented landscape.

METHODS

We used data of 975 wildcats genotyped at 14 microsatellites and an individual-based landscape genetic framework to assess the importance of twelve landscape variables for explaining observed genetic connectivity. For this, we optimized landscape resistance surfaces for all variables and compared their relative impacts using multiple regression on distance matrices and commonality analysis.

RESULTS

Genetic connectivity was best explained by a synergistic combination of six landscape variables and isolation by distance. Of these variables, road density had by far the strongest individual impact followed by synergistic effects of agricultural lands and settlements. Subsequent analyses involving different road types revealed that the strong effect of road density was largely due to state roads, while highways and federal roads had a much smaller, and county roads only a negligible impact.

MAIN CONCLUSIONS

Our results highlight that landscape-wide genetic connectivity in wildcats across Germany is strongly shaped by the density of roads and in particular state roads, with higher densities providing larger resistance to successful dispersal. These findings have important implications for conservation planning, as measures to mitigate fragmentation effects of roads (e.g., over- or underpasses) often focus on large, federally managed transportation infrastructures. While these major roads exert local barrier effects, other road types can be more influential on overall connectivity, as they are more abundant and more widespread across the landscape.

Lack of detectable genetic isolation in the cyclic rodent Microtus arvalis despite large landscape fragmentation owing to transportation infrastructures

Although roads are widely seen as dispersal barriers, their genetic consequences for animals that experience large fluctuations in population density are poorly documented. We developed a spatially paired experimental design to assess the genetic impacts of roads on cyclic voles (Microtus arvalis) during a high-density phase in North-Western Spain. We compared genetic patterns from 15 paired plots bisected by three different barrier types, using linear mixed models and computing effect sizes to assess the importance of each type, and the influence of road features like width or the age of the infrastructure. Evidence of effects by roads on genetic diversity and differentiation were lacking. We speculate that the recurrent (each 3-5 generations) episodes of massive dispersal associated with population density peaks can homogenize populations and mitigate the possible genetic impact of landscape fragmentation by roads. This study highlights the importance of developing spatially replicated experimental designs that allow us to consider the large natural spatial variation in genetic parameters. More generally, these results contribute to our understanding of the not well explored effects of habitat fragmentation on dispersal in species showing "boom-bust" dynamics.

Sensitivity of Tropical Insectivorous Birds to the Anthropocene: A Review of Multiple Mechanisms and Conservation Implications

Epigraph: “The house is burning. We do not need a thermometer. We need a fire hose.” (P. 102, Janzen and Hallwachs, 2019). Insectivorous birds are declining widely, and for diverse reasons. Tropical insectivorous birds, more than 60% of all tropical birds, are particularly sensitive to human disturbances including habitat loss and fragmentation, intensive agriculture and pesticide use, and climate change; and the mechanisms are incompletely understood. This review addresses multiple, complementary and sometimes synergistic explanations for tropical insectivore declines, by categorizing explanations into ultimate vs. proximate, and direct versus indirect. Ultimate explanations are diverse human Anthropocene activities and the evolutionary history of these birds. This evolutionary history, synthesized by the Biotic Challenge Hypothesis (BCH), explains tropical insectivorous birds' vulnerabilities to many proximate threats as a function of both these birds' evolutionary feeding specialization and poor dispersal capacity. These traits were favored evolutionarily by both the diversity of insectivorous clades competing intensely for prey and co-evolution with arthropods over long evolutionary time periods. More proximate, ecological threats include bottom-up forces like declining insect populations, top-down forces like meso-predator increases, plus the Anthropocene activities underlying these factors, especially habitat loss and fragmentation, agricultural intensification, and climate change. All these conditions peak in the lowland, mainland Neotropics, where insectivorous bird declines have been repeatedly documented, but also occur in other tropical locales and continents. This multiplicity of interacting evolutionary and ecological factors informs conservation implications and recommendations for tropical insectivorous birds: (1) Why they are so sensitive to global change phenomena is no longer enigmatic, (2) distinguishing ultimate versus proximate stressors matters, (3) evolutionary life-histories predispose these birds to be particularly sensitive to the Anthropocene, (4) tropical regions and continents vary with respect to these birds' ecological sensitivity, (5) biodiversity concepts need stronger incorporation of species' evolutionary histories, (6) protecting these birds will require more, larger reserves for multiple reasons, and (7) these birds have greater value than generally recognized.

Isolation and characterization of microsatellites for the endangered endemic tree Nothofagus alessandrii (Nothofagaceae)

Nothofagus alessandrii (Nothofagaceae) is one of the most endangered trees from Chile due to high rates of habitat disturbance caused by human activities. Despite its conservation status, few molecular markers are available to study its population genetic, connectivity and to assist reproduction programs. Thus, the species needs urgent actions to restore its original distribution. Novel polymorphic microsatellites from the genome of N. alessandrii were isolated and characterized using high-through sequencing. A total of 30 primer pairs were synthesized and 18 microsatellites were amplified correctly. Polymorphism and genetic diversity was evaluated in 58 individuals from three populations of N. alessandrii. Sixteen of them were polymorphic and the number of alleles in the pooled sample ranged from 2 to 14, the mean number of alleles was 4.81. The mean values of observed heterozigosity (H_O) and excepted heterozygosity (H_E) are similar in all studied populations. Linkage disequilibrium was found between a few pairs of loci (five out of 263 tests) suggesting that most of the markers can be considered as independent. Significant deviations from Hardy-Weinberg equilibrium (P < 0.05) were found in four loci probably due to low sampling size. Transferability to the congeneric N. pumilio was successful in only four out of the sixteen polymorphic markers. The microsatellite markers developed in this study will be useful to study the genetic diversity and structure and to develop integrated management plans for the conservation of this endangered species.

Current and Forthcoming Approaches for Benchmarking Genetic and Genomic Diversity

The current attrition of biodiversity extends beyond loss of species and unique populations to steady loss of a vast genomic diversity that remains largely undescribed. Yet the accelerating development of new techniques allows us to survey entire genomes ever faster and cheaper, to obtain robust samples from a diversity of sources including degraded DNA and residual DNA in the environment, and to address conservation efforts in new and innovative ways. Here we review recent studies that highlight the importance of carefully considering where to prioritize collection of genetic samples (e.g., organisms in rapidly changing landscapes or along edges of geographic ranges) and what samples to collect and archive (e.g., from individuals of little-known subspecies or populations, even of species not currently considered endangered). Those decisions will provide the sample infrastructure to detect the disappearance of certain genotypes or gene complexes, increases in inbreeding levels, and loss of genomic diversity as environmental conditions change. Obtaining samples from currently endangered, protected, and rare species can be particularly difficult, thus we also focus on studies that use new, non-invasive ways of obtaining genomic samples and analyzing them in these cases where other sampling options are highly constrained. Finally, biological collections archiving such samples face an inherent contradiction: their main goal is to preserve biological material in good shape so it can be used for scientific research for centuries to come, yet the technologies that can make use of such materials are advancing faster than collections can change their standardized practices. Thus, we also discuss current and potential new practices in biological collections that might bolster their usefulness for future biodiversity conservation research.

Macrogenetic studies must not ignore limitations of genetic markers and scale

Millette et al. (Ecology Letters, 2020, 23:55-67) reported no consistent worldwide anthropogenic effects on animal genetic diversity using repurposed mitochondrial DNA sequences. We reexamine data from this study, describe genetic marker and scale limitations which might lead to misinterpretations with conservation implications, and provide advice to improve future macrogenetic studies.

The inflated significance of neutral genetic diversity in conservation genetics

The current rate of species extinction is rapidly approaching unprecedented highs, and life on Earth presently faces a sixth mass extinction event driven by anthropogenic activity, climate change, and ecological collapse. The field of conservation genetics aims at preserving species by using their levels of genetic diversity, usually measured as neutral genome-wide diversity, as a barometer for evaluating population health and extinction risk. A fundamental assumption is that higher levels of genetic diversity lead to an increase in fitness and long-term survival of a species. Here, we argue against the perceived importance of neutral genetic diversity for the conservation of wild populations and species. We demonstrate that no simple general relationship exists between neutral genetic diversity and the risk of species extinction. Instead, a better understanding of the properties of functional genetic diversity, demographic history, and ecological relationships is necessary for developing and implementing effective conservation genetic strategies.