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230 results for “population decline”
Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across Indian subcontinent
<p><span><span><b><i>Background </i></b></span></span></p> <p><span><span>Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, <i>Panthera pardus</i>, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline. </span></span></p> <p><span><span><b><i>Methods </i></b></span></span></p> <p><span><span>We collected faecal samples from the Terai-Arc landscape of north India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities. </span></span></p> <p><span><span><b><i>Results </i></b></span></span></p> <p><span><span>Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75-90% population decline between ∼120-200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India. </span></span></p> <p><span><span><b><i>Conclusions </i></b></span></span></p> <p><span><span>Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.</span></span></p>
Data from: Early snowmelt projected to cause population decline in a subalpine plant
How climate change influences the dynamics of plant populations is not well understood, as few plant studies have measured responses of vital rates to climatic variables and modeled the impact on population growth. I used 25 years of demographic data to analyze how survival, growth, and fecundity respond to date of spring snow melt for a subalpine plant. Fecundity was estimated by seed production (over 15 years) and also divided into flower number, fruit set, seeds per fruit, and escape from seed predation. Despite no apparent effects on flower number, plants produced more seeds in years with later snowmelt. Survival and probability of flowering were reduced by early snow melt in the previous year. Based on demographic models, earlier snowmelt with warming is expected to lead to negative population growth, driven especially by changes in seedling establishment and seed production. These results provide a rare example of how climate change is expected to influence the dynamics of a plant population. They furthermore illustrate the potential for strong population impacts even in the absence of more commonly reported visual signs, such as earlier blooming or reduced floral display in early melting years.
Data from: Holocene population decline and conservation implication for the Western Hercules Beetle, Dynastes grantii (Coleoptera, Scarabaeidae)
The Western Hercules beetle (Dynastes grantii) is endemic to the highland forest habitats of southwestern USA and northern Mexico. The habitats harbor many endemic species, but are being threatened by rapid climate change and urban development. In this study, the genetic structure of D. grantii populations from southwestern USA was investigated. Specifically, genomic data from double-digest RADseq (ddRADseq) libraries were utilized to test whether geographically distant populations from the Mogollon Rim (Arizona [N = 12 individuals] and New Mexico [N = 10 individuals]) are genetically structured. The study also estimated the effective population size of the Mogollon Rim populations based on genetic diversity. The results indicated that the two geographic populations from the Mogollon Rim were not genetically structured. A population size reduction was detected since the end of the last glacial period, which coincided with a reduction of forest habitat in the study area. The results implied that the connectivity and the size of highland forest habitats in the Mogollon Rim could have been the major factors shaping the population genetic structure and demographic history of D. grantii. The Western Hercules beetle could be a useful flagship species for local natural history education and to promote the conservation of highland forest habitats.
Applying genomic approaches to identify historic population declines in European forest bats
<ol> <li>Anthropogenically-driven environmental changes over the past two centuries have led to severe biodiversity loss, most prominently in the form of loss of populations and individuals. Better tools are needed to assess the magnitude of these wildlife population declines. Anecdotal evidence suggests European bat populations have suffered substantial declines in the past few centuries. However, there is little empirical evidence of these declines that can be used to put more recent population changes into historic context and set appropriate targets for species recovery. </li> <li>This study is a collaboration between academics and conservation practitioners to develop molecular approaches capable of providing quantitative evidence of historic population changes and their drivers that can inform the assessment of conservation status and conservation management. We generated a genomic dataset for the Western barbastelle, <em>Barbastella barbastellus</em>, a globally Near Threatened and regionally Vulnerable bat species, including colonies from across the species' British and Iberian ranges. We used a combination of landscape genetics and approximate Bayesian computation model-based inference of demographic history to identify both evidence of population size changes and possible drivers of these changes. </li> <li>We found that levels of genetic diversity and inbreeding were related to broadleaf woodland cover around the colony location. Genetic connectivity was impeded by artificial lights and facilitated by the combination of rivers and broadleaf woodland cover. </li> <li>The demographic history analysis showed that both the northern and southern British barbastelle populations have declined by 99% over the past 330–548 years. These declines may have been triggered by loss of large oak trees and native woodlands due to shipbuilding during the early colonial period.</li> <li> <em>Synthesis and applications</em>. Genomic approaches can be applied to provide a better understanding of the conservation status of threatened species, within historic and contemporary context, and inform their conservation management. This study shows how we can bridge the implementation gap and promote the application of genomics in conservation management through co-designing studies with conservation practitioners and co-developing applied management targets and recommendations.</li> </ol>
Data and code from: Disentangling the drivers of decadal body size decline in an insect population
<p>While climate warming is widely predicted to reduce body size of ectotherms, evidence for this trend is mixed. Body size depends not only on temperature but also on other factors, such as food quality and intraspecific competition. Because temperature trends or other long-term environmental factors may affect population size and food sources, attributing trends in average body size to temperature requires the separation of potentially confounding effects. We evaluated trends in the body size of the midge <em>Tanytarsus gracilentus</em> and potential drivers (water temperature, population size, and food quality) between 1977 and 2015 at Lake Mývatn, Iceland. Although temperatures increased at Mývatn over this period, there was only a slight (non-significant) decrease in midge adult body size, contrary to theoretical expectations. Using a state-space model including multiple predictors, body size was negatively associated with both water temperature and midge population abundance, and it was positively associated with <sup>13</sup>C enrichment of midges (an indicator of favorable food conditions). The magnitude of these effects were similar, such that simultaneous changes in temperature, abundance, and carbon stable isotopic signature could counteract each other in the long-term body size trend. Our results illustrate how multiple factors, all of which could be influenced by global change, interact to affect average ectotherm body size.</p>
Data from: Genetic signatures of lineage fusion closely resemble population decline
<p>Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline—high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (<em>F</em><sub>S</sub> and <em>Z</em><sub>nS</sub>), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.</p>
Anthropogenic disturbance driving population decline of a dominant tree in East Asia evergreen broadleaved forests over the last 11,000 years
<p><span>Current biodiversity loss was generally considered to be caused by </span><span>anthropogenic disturbance</span><span>, but when anthropogenic activities began to impact biodiversity loss is still </span><span>controversial</span><span>. One hypothesis suggested it was from the industrial era, while others proposed that the anthropogenic disturbance had already resulted in biodiversity decline since the Early Holocene. To test these hypotheses, we focus on subtropical East Asia, which has witnessed a land use and anthropogenic history since the Early Holocene. We selected the unique vegetation of evergreen broadleaved forests (EBLFs), using a genomic approach to infer the demographic history of a dominant plant (<em>Litsea</em> <em>elongata</em>) of EBLFs, and to further detangle the impact of climate change and/or anthropogenic disturbance on effective population size fluctuation. Nine well-defined geographical clades were identified within extant populations of <em>L</em>. <em>elongata</em>. The estimated historical population sizes of these clades all contracted, indicating persistent population decline over the last 11,000 years. Significant correlation was detected between demographic history and three anthropogenic disturbance factors, rather than the climate change in the Holocene. Therefore, we provided the <span>dataset used for<span> phylo</span></span>g<span>enomic analysis</span>,<span> </span><span> demographic history inference</span><span>, and correlation analysis in this study.</span></span></p>
Population structure, patterns of natal dispersal, and demographic history in a declining aerial insectivore, the purple martin Progne subis
<p>Genetic variation is a fundamental component of biodiversity, and studying population structure, gene flow, and demographic history can help guide conservation strategies for many species. Like other aerial insectivores, the purple martin (<em>Progne subis</em>) is in decline, and yet their genetic background remains largely unknown. To address this knowledge gap, we assessed population structure in the nominate eastern subspecies (<em>P. s. subis</em>) with relation to natal dispersal and examined historical genetic patterns in all three subspecies (<em>P. s. subis, P. s. arboricola, P. s. hesperia</em>) across their North American breeding range by estimating effective population sizes over time. We used next-generation sequencing strategies for genomic analyses, integrating whole-genome resequencing data with continent-wide band encounter records to examine natal dispersal. We documented population structure across <em>P. s. subis</em>, with the highest differentiation between the northern (Alberta) and more southern colonies and following patterns of isolation-by-distance. Consistent with spatial patterns of genetic differentiation, we also found greater longitudinal than latitudinal natal dispersal distances, signifying potential latitudinal constraints on gene flow. Earlier contractions in effective population sizes in the western <em>P. s. arboricola</em> and <em>P. s. hesperia</em> compared to the eastern <em>P. s. subis</em> subspecies suggest these subspecies originated from two different glacial refugia. Together, these findings support latitudinal distinction in <em>P. s. subis</em>, and elucidate the origin of subspecies differentiation, highlighting the importance to conserve populations across the range to maximize genetic diversity and adaptive potential in the purple martin.</p>
Data from: Historical surveys reveal a long-term decline in muskrat populations
<p>The muskrat (<i>Ondatra zibethicus</i>) is an iconic species in Canada, valued for both its fur and its integral role in wetland ecosystems, and widely regarded for its perseverance. However, the resilience of this semi-aquatic mammal seems to be in question now as increasing evidence points to widespread population declines. Recent analyses of harvest data across North America suggest a reduction in their numbers, but this has not been widely corroborated by population surveys. In this study we replicated historic muskrat house count surveys at two large Great Lakes coastal wetlands and present confirmation that declines in muskrat harvest correspond to actual declines in muskrat abundance. At the Point Pelee National Park marsh and the Matchedash Bay-Gray Marsh wetland we found that mean muskrat house counts declined by 93% and 91% respectively between historic surveys 40-50 years ago and contemporary surveys over the past seven years. The factors responsible for these dramatic declines remain unclear but there may be a relationship with changes in the habitat quality of these wetlands that have occurred over the same time frame. Not only is the loss of muskrats an issue for the resulting loss of the wetland ecosystem services they provide, but it may be an indication of broader marsh ecosystem degradation. As such, a scarcity of muskrats should be considered a red flag for the state of biodiversity in our wetlands. Continued surveys and ongoing research are needed to shed more light on the current status of muskrat populations and their marsh habitats across their native range.</p>
Population analysis of retrotransposons in giraffe genomes supports RTE decline and widespread LINE1 activity in Giraffidae
<p>The majority of structural variation in genomes is caused by insertions of transposable elements (TEs). In mammalian genomes, the main TE fraction is made up of autonomous and non-autonomous non-LTR retrotransposons commonly known as LINEs and SINEs (Long and Short Interspersed Nuclear Elements). Here we present one of the first population-level analysis of TE insertions in a non-model organism, the giraffe. Giraffes are ruminant artiodactyls, one of the few mammalian groups with genomes that are colonized by putatively active LINEs of two different clades of non-LTR retrotransposons, namely the LINE1 and RTE/BovB LINEs as well as their associated SINEs. We analyzed TE insertions of both types, and their associated SINEs in three giraffe genome assemblies, as well as across a population level sampling of 48 individuals covering all extant giraffe species. Results The comparative genome screen identified 139,525 recent LINE1 and RTE insertions in the sampled giraffe population. The analysis revealed a drastically reduced RTE activity in giraffes, whereas LINE1 is still actively propagating in the genomes of extant (sub)-species. In concert with the extremely low activity of the giraffe RTE, we also found that RTE-dependent SINEs, namely Bov-tA and Bov-A2, have been virtually immobile in the last 2 million years. Despite the high current activity of the giraffe LINE1, we did not find evidence for the presence of currently active LINE1-dependent SINEs. TE insertion heterozygosity rates differ among the different (sub)-species, likely due to divergent population histories. Conclusions The horizontally transferred RTE/BovB and its derived SINEs appear to be close to inactivation and subsequent extinction in the genomes of extant giraffe species. This is the first time that the decline of a TE family has been meticulously analyzed from a population genetics perspective. Our study shows how detailed information about past and present TE activity can be obtained by analyzing large-scale population-level genomic data sets.</p>
Grassland bird population declines at three Breeding Bird Survey spatial scales in contrast to a large native prairie
<p>Grassland biomes in North America are threatened by agricultural intensification with implications for grassland associated bird populations via habitat loss, alteration, pesticide use and declining landscape heterogeneity. Despite decades of conservation concern, steep declines of North American grassland bird populations continue. Key to optimizing conservation effort is understanding how land-use practices, such as agriculture, across the annual cycle affects population status. Determining the relative influence of impacts on grassland bird declines is difficult given that the most robust estimates of population trends, the North American Breeding Bird Survey (BBS), are from surveys throughout agriculturally dominated regions. Our goal was to explore whether agriculture during the breeding season is a major driver of grassland bird declines. We derived trends for 16 grassland bird species spanning 23 years (1994-2016) at a large (459 km2), native prairie site, Suffield National Wildlife Area (SNWA) in Alberta, Canada. We compared those trends to the BBS across three spatial scales, a regional monitoring scheme with higher than average native grass cover (GBM), BCR 11 - Canada (Canada) and all of BCR 11 (BCR 11). Trends measured as annual percent change and credible interval varied greatly among species and survey strata. Across all species, declines were greatest for Canada (-1.3%, CI: -2.8, 0.0) and BCR 11 (-1.9%, CI: -3.2, -0.6). This contrasts with positive mean trends for GBM routes (1.0%, CI: -0.4, 2.3) and the SNWA data (1.7%, CI: 0.3, 3.3). Six of 16 species at SNWA were increasing with one decreasing. Five species increased at GBM and four declined. Canada had 10 species declines and three increases and BCR 11 had 10 declines and no increases. None of six grassland obligate species declined at SNWA, two declined at GBM, and all six declined over the two larger BBS strata. Our results showing fewer negative population trends at a large native grassland site compared to BBS at three spatial scales across the North American prairies support the prediction that agricultural intensification on breeding grounds is a major driver of declining populations and protection of remaining native grasslands should remain a key component of grassland bird conservation efforts.</p>
Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads
<p>Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (<em>Dasyurus hallucatus</em>), an Endangered marsupial carnivore. We used next-generation sequencing methods to genotype 10,191 SNPs in 352 individuals from across a 3220 km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterised by (1) biogeographic barriers driving hierarchical population structure through long-term isolation, and (2) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (<em>Rhinella marina</em>). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterisation of putative evolutionarily significant units.</p>
Replication data for: Demographic declines and responses of breeding bird populations to human footprint in the Athabasca Oil Sands Region, Alberta, Canada
<p class="MsoNormal">This data package includes data files and an R script to reproduce results reported in the paper "Demographic declines and responses of breeding bird populations to human footprint in the Athabasca Oil Sands Region, Alberta, Canada". Analyses include hierarchical multispecies models applied to data from 31 bird species at 38 Monitoring Avian Productivity and Survivorship (MAPS) stations to assess 10-year (2011–2020) demographic trends and responses to energy sector disturbance (human footprint proportion) in the Athabasca oil sands region of Alberta, Canada. Adult captures, productivity, and residency probability all declined over the study period, and adult apparent survival probability also tended to decline. Trends in adult captures, productivity, and survival were all more negative at stations with larger increases in disturbance over the study period. Species associated with early seral stages were more commonly captured at more disturbed stations, while species typical of mature forests were more commonly captured at less disturbed stations. Productivity was positively correlated with disturbance within 5 km of stations after controlling for disturbance within 1 km of stations. Adult apparent survival showed relatively little response to disturbance; stresses experienced beyond the breeding grounds likely play a larger role in influencing survival. Residency probability was negatively related to disturbance within 1-km scale of stations and could reflect processes affecting the ability of birds to establish or maintain territories in disturbed landscapes.</p>
Data from: Maternal diet influences fecundity in a freshwater turtle undergoing population decline
<p>Food availability determines the amount of energy animals can acquire and allocate to reproduction and other necessary functions. Female animals that are food-limited thus experience reduced energy available for reproduction. When this occurs, females may reduce frequency of reproductive events or the number or size of offspring per reproductive bout. We assessed how maternal diet affects reproductive output in adult female Murray River short-necked turtles, <em>Emydura macquarii,</em> from four wetlands in Victoria. We previously found that turtle diets differ in the composition of plants and animals between our study wetlands. In this study, we tested whether differences in turtle diet composition (i.e plants and animals) at these wetlands were associated with differences in clutch mass, individual egg mass, bulk egg composition, and hatching success. We found total clutch mass increased with maternal body size at each site. At sites where filamentous green algae were scarce and <em>E. macquarii</em> were carnivorous, females produced smaller clutches relative to body size compared to females from sites where algae were abundant, and turtles were more herbivorous. Individual egg mass, bulk egg composition, and hatching success did not differ across wetlands. Isotopic analysis revealed a significant positive relationships between the carbon and nitrogen isotopes (δ<sup>13</sup>C, δ<sup>15</sup>N) of the eggs and those of the mothers, indicating that mothers allocated ratios of carbon and nitrogen isotopes to their eggs similar to those present in their tissues. Our study suggests that at sites where females are more carnivorous due to a relative absence of algae, females produce smaller clutches but other aspects of their reproduction are not significantly impacted. The reduction in clutch size associated with differences in the availability of dietary plants and animals may have long-term consequences for <em>E. macquarii</em> and other freshwater turtle species that are experiencing population declines.</p>
Fig. 4 in Age Structure In A Declining Population Of Rana Temporaria From Northern Italy
Fig. 4. Age distribution of male (filled bars) and female (empty bars) Rana temporaria
Reversing the decline of threatened koala (Phascolarctos cinereus) populations in New South Wales: Using genomics to enhance conservation outcomes
<p>Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction-based method (DArTSeq), we generated a data set of 3,239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (<em>Phascolarctos cinereus</em>), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range.<strong> </strong>Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned amongst individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.</p>
Fig. 1 in Trypanosomes genetic diversity, polyparasitism and the population decline of the critically endangered Australian marsupial, the brush tailed bettong or woylie (Bettongia penicillata)
Fig. 1. Geographical origin of the different species of marsupials trapped in this study.
Fig. 2 in Ectoparasites are unlikely to be a primary cause of population declines of bent-winged bats in south-eastern Australia
Fig. 2. Dorsal view of Penicillidia oceanica. Note absence of notopleural setae (Arrow).
Fig. 1 in Ectoparasites are unlikely to be a primary cause of population declines of bent-winged bats in south-eastern Australia
Fig. 1. Dorsal view of Penicillidia tectisentis. Note notopleural setae (Arrow).
Figure 1 in Is the global decline reflects local declines? A case of the population trend of Far Eastern Curlew Numenius madagascariensis in Banyuasin Peninsula, South Sumatra, Indonesia
Figure 1. Map of Banyuasin Peninsula, South Sumatra, Indonesia.
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