scholarly journals The Demographic History of Micro-endemics: Have Rare Species Always Been Rare?

2020 ◽  
Author(s):  
Andrew J. Helmstetter ◽  
Stuart Cable ◽  
Franck Rakotonasolo ◽  
Romer Rabarijaona ◽  
Mijoro Rakotoarinivo ◽  
...  
Keyword(s):  
Threatened Species ◽  
Rare Species ◽  
Extinction Risk ◽  
Demographic History ◽  
Population Decline ◽  
Rapid Decline ◽  
Conservation Assessment ◽  
History Of ◽  
Narrow Endemics ◽  
Data Deficient

AbstractExtinction has increased as human activities impact ecosystems. Conservation assessments for the IUCN red list are a fundamental tool in aiding the prevention of further extinction, yet, relatively few species have been thoroughly assessed. To increase the efficiency of assessments, novel approaches are needed to highlight threatened species that are currently data deficient. Many Madagascan plant species currently have extremely narrow ranges, but this may not have always been the case. To assess this, we used high-throughput DNA sequencing for 2-5 individuals of each species - reflecting the paucity of samples available for rare species. We estimated effective population size (Ne) for each species and compared this to census population (Nc) sizes when known. In each case, Ne was an order of magnitude larger than Nc – a signature of rapid, recent population decline. We then estimated the demographic history of each species, tracking changes in Ne over time. Five out of ten species displayed significant population declines towards the present (68–90% decreases). Our results for palm trees indicate that it is possible to predict extinction risk, particularly in the most threatened species. We performed simulations to show that our approach has the power to detect population decline during the Anthropocene, but performs less well when less data is used. Similar declines to those in palms were observed in data deficient species or those assessed as of least concern. These analyses reveal that Madagascar’s narrow endemics were not always rare, having experienced rapid decline in their recent history. Our approach offers the opportunity to target species in need of conservation assessment with little prior information, particularly in regions where human modification of the environment has been rapid.SummaryCurrent IUCN conservation assessment methods are reliant on observed declines in species population and range sizes over the last one hundred years, but for the majority of species this information is not available. We used a population genetic approach to reveal historical demographic decline in the rare endemic flora of Madagascar. These results show that it is possible to predict extinction risk from demographic patterns inferred from genetic data and that destructive human influence is likely to have resulted in the very high frequency of narrow endemics present on the island. Our approach will act as an important tool for rapidly assessing the threatened status of poorly known species in need of further study and conservation, particularly for tropical flora and fauna.

scholarly journals The demographic history of Madagascan micro-endemics: have rare species always been rare?

2021 ◽  
Vol 288 (1959) ◽  
pp. 20210957
Author(s):  
Andrew J. Helmstetter ◽  
Stuart Cable ◽  
Franck Rakotonasolo ◽  
Romer Rabarijaona ◽  
Mijoro Rakotoarinivo ◽  
...  
Keyword(s):  
Plant Species ◽  
Threatened Species ◽  
Sequence Data ◽  
Extinction Risk ◽  
Demographic History ◽  
Population Decline ◽  
Rapid Decline ◽  
Effective Population ◽  
Conservation Assessment ◽  
Data Deficient

Extinction has increased as human activities impact ecosystems, yet relatively few species have conservation assessments. Novel approaches are needed to highlight threatened species that are currently data-deficient. Many Madagascan plant species have extremely narrow ranges, but this may not have always been the case—it is unclear how the island's diverse flora evolved. To assess this, we generated restriction-site associated DNA sequence data for 10 Madagascan plant species, estimated effective population size ( N e ) for each species and compared this to census ( N c ) sizes. In each case, N e was an order of magnitude larger than N c —signifying rapid, recent population decline. We then estimated species' demographic history, tracking changes in N e over time. We show that it is possible to predict extinction risk, particularly in the most threatened species. Furthermore, simulations showed that our approach has the power to detect population decline during the Anthropocene. Our analyses reveal that Madagascar's micro-endemics were not always rare, having experienced a rapid decline in their recent history. This casts further uncertainty over the processes that generated Madagascar's exceptional biodiversity. Our approach targets data-deficient species in need of conservation assessment, particularly in regions where human modification of the environment has been rapid.

scholarly journals Global extinction risk for seahorses, pipefishes and their near relatives (Syngnathiformes)

Oryx ◽  
2021 ◽  
pp. 1-10
Author(s):  
Riley A. Pollom ◽  
Gina M. Ralph ◽  
Caroline M. Pollock ◽  
Amanda C.J. Vincent
Keyword(s):  
Threatened Species ◽  
Habitat Degradation ◽  
Extinction Risk ◽  
Conservation Status ◽  
Field Research ◽  
Selective Extraction ◽  
Iucn Red List ◽  
Point Estimate ◽  
Conservation Action ◽  
Data Deficient

Abstract Few marine taxa have been comprehensively assessed for their conservation status, despite heavy pressures from fishing, habitat degradation and climate change. Here we report on the first global assessment of extinction risk for 300 species of syngnathiform fishes known as of 2017, using the IUCN Red List criteria. This order of bony teleosts is dominated by seahorses, pipefishes and seadragons (family Syngnathidae). It also includes trumpetfishes (Aulostomidae), shrimpfishes (Centriscidae), cornetfishes (Fistulariidae) and ghost pipefishes (Solenostomidae). At least 6% are threatened, but data suggest a mid-point estimate of 7.9% and an upper bound of 38%. Most of the threatened species are seahorses (Hippocampus spp.: 14/42 species, with an additional 17 that are Data Deficient) or freshwater pipefishes of the genus Microphis (2/18 species, with seven additional that are Data Deficient). Two species are Near Threatened. Nearly one-third of syngnathiformes (97 species) are Data Deficient and could potentially be threatened, requiring further field research and evaluation. Most species (61%) were, however, evaluated as Least Concern. Primary threats to syngnathids are (1) overexploitation, primarily by non-selective fisheries, for which most assessments were determined by criterion A (Hippocampus) and/or (2) habitat loss and degradation, for which assessments were determined by criterion B (Microphis and some Hippocampus). Threatened species occurred in most regions but more are found in East and South-east Asia and in South African estuaries. Vital conservation action for syngnathids, including constraining fisheries, particularly non-selective extraction, and habitat protection and rehabilitation, will benefit many other aquatic species.

scholarly journals Comparing maternal genetic variation across two millennia reveals the demographic history of an ancient human population in southwest Turkey

2016 ◽  
Vol 3 (2) ◽  
pp. 150250 ◽  
Author(s):  
Claudio Ottoni ◽  
Rita Rasteiro ◽  
Rinse Willet ◽  
Johan Claeys ◽  
Peter Talloen ◽  
...  
Keyword(s):  
Demographic History ◽  
Population Decline ◽  
Fifth Century ◽  
Seventh Century ◽  
Human Occupation ◽  
Dna Variation ◽  
Genetic Discontinuity ◽  
History Of ◽  
The City ◽  
Modern Sample

More than two decades of archaeological research at the site of Sagalassos, in southwest Turkey, resulted in the study of the former urban settlement in all its features. Originally settled in late Classical/early Hellenistic times, possibly from the later fifth century BCE onwards, the city of Sagalassos and its surrounding territory saw empires come and go. The Plague of Justinian in the sixth century CE, which is considered to have caused the death of up to a third of the population in Anatolia, and an earthquake in the seventh century CE, which is attested to have devastated many monuments in the city, may have severely affected the contemporary Sagalassos community. Human occupation continued, however, and Byzantine Sagalassos was eventually abandoned around 1200 CE. In order to investigate whether these historical events resulted in demographic changes across time, we compared the mitochondrial DNA variation of two population samples from Sagalassos (Roman and Middle Byzantine) and a modern sample from the nearby town of Ağlasun. Our analyses revealed no genetic discontinuity across two millennia in the region and Bayesian coalescence-based simulations indicated that a major population decline in the area coincided with the final abandonment of Sagalassos, rather than with the Plague of Justinian or the mentioned earthquake.

scholarly journals Genomic evidence for the Old divergence of Southern European wolf populations

2020 ◽  
Vol 287 (1931) ◽  
pp. 20201206
Author(s):  
Pedro Silva ◽  
Marco Galaverni ◽  
Diego Ortega-Del Vecchyo ◽  
Zhenxin Fan ◽  
Romolo Caniglia ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Common Ancestor ◽  
Demographic History ◽  
Population Decline ◽  
Divergence Times ◽  
Single Population ◽  
History Of ◽  
Fragmented Distribution ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The grey wolf ( Canis lupus ) is one of the most widely distributed mammals in which a variety of distinct populations have been described. However, given their currently fragmented distribution and recent history of human-induced population decline, little is known about the events that led to their differentiation. Based on the analysis of whole canid genomes, we examined the divergence times between Southern European wolf populations and their ancient demographic history. We found that all present-day Eurasian wolves share a common ancestor ca 36 000 years ago, supporting the hypothesis that all extant wolves derive from a single population that subsequently expanded after the Last Glacial Maximum. We also estimated that the currently isolated European populations of the Iberian Peninsula, Italy and the Dinarics-Balkans diverged very closely in time, ca 10 500 years ago, and maintained negligible gene flow ever since. This indicates that the current genetic and morphological distinctiveness of Iberian and Italian wolves can be attributed to their isolation dating back to the end of the Pleistocene, predating the recent human-induced extinction of wolves in Central Europe by several millennia.

scholarly journals One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Thais M. Teixeira ◽  
Alison G. Nazareno
Keyword(s):  
Genetic Diversity ◽  
Missing Data ◽  
Plant Species ◽  
Threatened Species ◽  
Demographic History ◽  
Small Population ◽  
Narrow Endemic ◽  
Population Genomic ◽  
Genomic Study ◽  
History Of

Intraspecific genetic variation plays a fundamental role in maintaining the evolutionary potential of wild populations. Hence, the assessment of genetic diversity patterns becomes essential to guide biodiversity conservation policies, particularly for threatened species. To inform management strategies for conservation of Mimosa catharinensis – a narrow endemic, critically endangered plant species – we identified 1,497 unlinked SNP markers derived from a reduced representation sequencing method (i.e., double digest restriction site associated DNA sequencing, or ddRADseq). This set of molecular markers was employed to assess intrapopulation genetic parameters and the demographic history of one extremely small population of M. catharinensis (N=33) located in the Brazilian Atlantic Forest. Contrary to what is expected for narrow endemic and threatened species with small population sizes, we observed a moderate level of genetic diversity for M. catharinensis [uHE(0%missing data)=0.205, 95% CI (0.160, 0.250); uHE(30%missing data)=0.233, 95% CI (0.174, 0.292)]. Interestingly, M. catharinensis, which is a lianescent shrub with no indication of seed production for at least two decades, presented high levels of outcrossing [t(0%missing data)=0.883, SE±0.0483; t(30%missing data)=0.909, SE±0.011] and an apparent absence of inbreeding [F(0%missing data)=−0.145, 95% CI (−0.189, −0.101); F(30%missing data)=−0.105, 95% CI (−0.199, −0.011)]. However, the reconstruction of demographic history of M. catharinensis indicated that the population should be suffered a recent bottleneck. Our population genomic study tackles a central issue in evolution and conservation biology and we expect that it will be useful to help safeguard the remaining genetic diversity reported for this unique genetic resource.

Justification for continued conservation efforts following the delisting of a threatened species: a case study of the woylie, Bettongia penicillata ogilbyi (Marsupialia:Potoroidae)

2010 ◽  
Vol 37 (3) ◽  
pp. 183 ◽  
Author(s):  
Christine Groom
Keyword(s):  
Threatened Species ◽  
Conservation Status ◽  
Population Decline ◽  
Population Monitoring ◽  
Rapid Decline ◽  
Successful Implementation ◽  
Bettongia Penicillata ◽  
Species Lists ◽  
Iucn Criteria

Context. There are few cases where a species has been removed from a list of threatened species as a result of conservation efforts. One such example is the woylie (also known as the brush-tailed bettong), Bettongia penicillata ogilbyi, which was removed from state (Western Australian), national (Australian) and international lists in 1996, following the successful implementation of the species’ recovery plan. Since downgrading of its conservation status, the woylie has been considered conservation dependent. Conservation efforts continued in the form of toxic baiting to control the species’ principal predator, monitoring to identify trends in distribution and abundance, and translocation to help restore ecosystem function and further secure the conservation status of the species. Recent observations of a decline in abundance of the species have prompted a review of its conservation status. Aims. To assess the conservation status of the woylie in 2006 against IUCN criteria and to investigate the value of continued conservation efforts following the delisting of the species. Methods. Monitoring data were collated and parameters required to assess the conservation status of the woylie against IUCN criteria were investigated. The various processes associated with conserving the species, such as translocation and monitoring, were also assessed. Key results. The species underwent a rapid decline between 2001 and 2006, reducing the population by ~75% to an estimated 10 000 individuals. The decline has not been consistent across occurrences and of particular concern are the declines observed at Perup/Lake Muir, Dryandra and Batalling, which were previously considered amongst the largest and most stable occurrences. In 2006, the species qualified for listing as Endangered using IUCN criteria. The resources allocated to translocation and monitoring the delisted woylie have ultimately resulted in managers being in a much better position to understand and act when an unforeseeable population decline occurred. Conclusion. Conservation efforts and population monitoring of delisted species must continue at a level where changes in distribution or abundance, which are significant enough to support relisting, can be detected. Implications. Threatened species lists should not be the primary consideration in allocation of resources to conservation efforts.

scholarly journals Low genetic diversity, restricted dispersal, and elevation-specific patterns of population decline in American pikas in an atypical environment

2015 ◽  
Vol 97 (2) ◽  
pp. 464-472 ◽  
Author(s):  
Kelsey M. Robson ◽  
Clayton T. Lamb ◽  
Michael A. Russello
Keyword(s):  
Climate Change ◽  
Extinction Risk ◽  
Demographic History ◽  
Mammalian Species ◽  
Population Decline ◽  
Elevational Gradient ◽  
High Elevation ◽  
Population Connectivity ◽  
Genetic Characteristics ◽  
Range Core

Abstract In the face of climate change, there is a growing need for research into the ability of organisms to persist at the limits of their bioclimatic envelope. American pikas ( Ochotona princeps ) have emerged as a focal mammalian species for investigating extinction risk related to climate change; however, most studies have occurred in characteristic alpine talus habitat within the range core. In the Columbia River Gorge (CRG), Oregon, American pikas inhabit low-elevation talus slopes previously considered outside the species’ bioclimatic range. We used microsatellite genotypic data to reconstruct levels of genetic variation, population connectivity, and demographic history at 11 CRG sites spanning an elevational gradient (104–1,292 m). Sampled sites separated into 2 genetic clusters largely explained by elevation, topography, and geographic proximity, with pairwise estimates of differentiation and migration rates suggesting little gene flow may be occurring. Sites were characterized by levels of allelic richness and heterozygosity substantially lower than values reported at characteristic alpine sites from the range core. Evidence of recent demographic contraction was found almost exclusively at high-elevation sites despite these areas being considered refuges from climate warming in more typical habitat. Given their unique genetic characteristics and persistence in an atypical environment, the CRG pika populations likely constitute a significant component of intraspecific biodiversity with high conservation value.

scholarly journals A National assessment of aichi biodiversity target 12 – an international conservation initiative

2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Kirandeep K Dhami
Keyword(s):  
Threatened Species ◽  
Biological Diversity ◽  
Extinction Risk ◽  
Conservation Status ◽  
Population Decline ◽  
National Assessment ◽  
The Status ◽  
Aichi Biodiversity Targets ◽  
Conservation Plans ◽  
Taking Action

The Aichi Biodiversity targets are a set of twenty targets for the Convention of Biological Diversity (CBD) that were developed with the intention to help each participating country to measure the progress made in preventing the loss of biological diversity. These targets provide a 10-year period for taking action by the countries. These targets setup in 2010 are expected to be achieved within 2020 by all the 193 countries signatory to CBD. Aichi Biodiversity Target 12 is considered to be one of the most important targets, which is directly or indirectly linked to all of the other 19 CBD Targets. Aichi-12 sets up the goal for each country to prevent the extinction of known threatened species and improve the conservation status of those species that are on decline. This target calls for establishment of conservation plans for species that face a high risk to extinction. Hence, it is of urgent need to understand the extinction risk posed to each of the threatened species in the country and the factors that are responsible for the population decline in species. Therefore, it is important for taking initiatives to remove/reduce those factors posing risk to the survival of species. This study presents a brief overview of the status and progress made by India towards achievement of Aichi-12.

Assessing rarity and threat in an arid-zone flora

2011 ◽  
Vol 59 (4) ◽  
pp. 336 ◽  
Author(s):  
J. L. Silcock ◽  
R. J. Fensham ◽  
T. G. Martin
Keyword(s):  
Threatened Species ◽  
Arid Zone ◽  
Extinction Risk ◽  
Plant Conservation ◽  
Life Forms ◽  
Plant Biology ◽  
The Status ◽  
Narrow Endemics ◽  
Threatening Processes ◽  
Current List

An understanding of rarity and how it relates to extinction risk is a central concern of conservation biology. Classic conceptions of rarity revolve around spatial rarity, based on distribution and abundance, rather than temporal rarity, where species may be common following certain conditions but rare for most of the time. This form of rarity is likely to be especially prevalent in highly variable arid systems. Rarity in the arid zone is also characterised by poorly understood threats, such as grazing, and may also reflect low collection effort given the vast and inaccessible areas involved. This study explores rarity and threat in the arid zone, based on the flora of a large region of western Queensland. The status of all species known to occur in the study area was systematically assessed, and the current list of threatened species was examined for bias in forms of rarity, life forms and habitats. Five threat syndromes were identified, arising from the interaction of plant biology and threatening processes. Over 60 potentially threatened species have been overlooked in the listing process. The list is dominated by narrow endemics from residual and spring habitats and the species from springs at least are genuinely threatened. Widespread but sparsely occurring species are under-represented in the current list, as are grasses. With the exception of spring-dependent species, plant conservation in western Queensland is currently constrained by lack of basic data on distribution, abundance, population dynamics and realistic threat syndromes for nearly all species. Separating the influence of genuine rarity, temporal rarity and low collection effort, as well as a more detailed understanding of threatening processes are needed to address plant conservation in the arid zone.

scholarly journals Reference genome and demographic history of the most endangered marine mammal, the vaquita

2020 ◽  
Author(s):  
Phillip A. Morin ◽  
Frederick I. Archer ◽  
Catherine D. Avila ◽  
Jennifer R. Balacco ◽  
Yury V. Bukhman ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Marine Mammal ◽  
Reference Genome ◽  
Demographic History ◽  
Mammalian Species ◽  
Small Population ◽  
Chromosome Length ◽  
Rapid Decline ◽  
History Of

AbstractThe vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

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