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

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.

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

10.1101/2020.03.10.985853 ◽

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.

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

Oryx ◽

10.1017/s0030605320000782 ◽

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.

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A third of the tropical African flora is potentially threatened with extinction

Science Advances ◽

10.1126/sciadv.aax9444 ◽

2019 ◽

Vol 5 (11) ◽

pp. eaax9444 ◽

Cited By ~ 22

Author(s):

T. Stévart ◽

G. Dauby ◽

P. P. Lowry ◽

A. Blach-Overgaard ◽

V. Droissart ◽

...

Keyword(s):

Plant Species ◽

Extinction Risk ◽

Vascular Plant ◽

Terrestrial Ecosystems ◽

Iucn Red List ◽

Conservation Priorities ◽

Conservation Assessment ◽

Continental Scale ◽

Tropical Plant ◽

African Flora

Preserving tropical biodiversity is an urgent challenge when faced with the growing needs of countries. Despite their crucial importance for terrestrial ecosystems, most tropical plant species lack extinction risk assessments, limiting our ability to identify conservation priorities. Using a novel approach aligned with IUCN Red List criteria, we conducted a continental-scale preliminary conservation assessment of 22,036 vascular plant species in tropical Africa. Our results underline the high level of extinction risk of the tropical African flora. Thirty-three percent of the species are potentially threatened with extinction, and another third of species are likely rare, potentially becoming threatened in the near future. Four regions are highlighted with a high proportion (>40%) of potentially threatened species: Ethiopia, West Africa, central Tanzania, and southern Democratic Republic of the Congo. Our approach represents a first step toward data-driven conservation assessments applicable at continental scales providing crucial information for sustainable economic development prioritization.

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A globally threatened shark, Carcharias taurus, shows no population decline in South Africa

Scientific Reports ◽

10.1038/s41598-020-75044-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Juliana D. Klein ◽

Aletta E. Bester-van der Merwe ◽

Matthew L. Dicken ◽

Arsalan Emami-Khoyi ◽

Kolobe L. Mmonwa ◽

...

Keyword(s):

South Africa ◽

Census Data ◽

Demographic History ◽

Conservation Status ◽

Population Decline ◽

Multilocus Genotype ◽

Population Declines ◽

Effective Population ◽

Anthropogenic Pressures ◽

Carcharias Taurus

Abstract Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark, Carcharias taurus (also known as the sandtiger or grey nurse shark), is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, we found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.730258 ◽

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.

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Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

10.1101/210054 ◽

2017 ◽

Author(s):

Erik M. Volz ◽

Xavier Didelot

Keyword(s):

Growth Rate ◽

Population Size ◽

Effective Population Size ◽

Growth Rates ◽

Sequence Data ◽

Demographic History ◽

Parametric Models ◽

Effective Population ◽

Epidemic Dynamics ◽

Non Parametric

AbstractNon-parametric population genetic modeling provides a simple and flexible approach for studying demographic history and epidemic dynamics using pathogen sequence data. Existing Bayesian approaches are premised on stationary stochastic processes which may provide an unrealistic prior for epidemic histories which feature extended period of exponential growth or decline. We show that non-parametric models defined in terms of the growth rate of the effective population size can provide a more realistic prior for epidemic history. We propose a non-parametric autoregressive model on the growth rate as a prior for effective population size, which corresponds to the dynamics expected under many epidemic situations. We demonstrate the use of this model within a Bayesian phylodynamic inference framework. Our method correctly reconstructs trends of epidemic growth and decline from pathogen genealogies even when genealogical data is sparse and conventional skyline estimators erroneously predict stable population size. We also propose a regression approach for relating growth rates of pathogen effective population size and time-varying variables that may impact the replicative fitness of a pathogen. The model is applied to real data from rabies virus and Staphylococcus aureus epidemics. We find a close correspondence between the estimated growth rates of a lineage of methicillin-resistant S. aureus and population-level prescription rates of β-lactam antibiotics. The new models are implemented in an open source R package called skygrowth which is available at https://mrc-ide.github.io/skygrowth/.

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Holocene Population Decline and Conservation Implication for the Western Hercules Beetle, Dynastes grantii (Coleoptera, Scarabaeidae)

Journal of Heredity ◽

10.1093/jhered/esz036 ◽

2019 ◽

Vol 110 (5) ◽

pp. 629-637 ◽

Cited By ~ 1

Author(s):

Jen-Pan Huang

Keyword(s):

United States ◽

Genetic Structure ◽

Population Size ◽

Demographic History ◽

Population Decline ◽

Southwestern United States ◽

Effective Population ◽

Mogollon Rim ◽

Major Factors ◽

Forest Habitats

Abstract The Western Hercules beetle (Dynastes grantii) is endemic to the highland forest habitats of southwestern United States 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 United States was investigated. Specifically, genomic data from double-digest restriction-site-associated DNA sequencing 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 2 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.

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

Wildlife Research ◽

10.1071/wr09129 ◽

2010 ◽

Vol 37 (3) ◽

pp. 183 ◽

Cited By ~ 26

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.

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

Journal of Mammalogy ◽

10.1093/jmammal/gyv191 ◽

2015 ◽

Vol 97 (2) ◽

pp. 464-472 ◽

Cited By ~ 13

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.

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Genomic stability through time despite decades of exploitation in cod on both sides of the Atlantic

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2025453118 ◽

2021 ◽

Vol 118 (15) ◽

pp. e2025453118

Author(s):

Malin L. Pinsky ◽

Anne Maria Eikeset ◽

Cecilia Helmerson ◽

Ian R. Bradbury ◽

Paul Bentzen ◽

...

Keyword(s):

Atlantic Cod ◽

Sequence Data ◽

Genomic Variation ◽

Whole Genome Sequence ◽

Phenotypic Change ◽

Rapid Decline ◽

Effective Population ◽

Genomic Change ◽

Early 21St Century ◽

Intensive Exploitation

The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod (Gadus morhua) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery.

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