Conservation priorities in an endangered estuarine seahorse are informed by demographic history

AbstractHistorical demographic events shape genetic diversity that remains evident in the genomes of contemporary populations. In the case of species that are of conservation concern, this information helps to unravel evolutionary histories that can be critical in guiding conservation efforts. The Knysna seahorse, Hippocampus capensis, is the world’s most endangered seahorse species, and it presently survives in only three estuaries on the South African south coast. Factors that contributed to the species becoming endangered are unclear; additionally, the lack of information on whether the three populations should be managed separately because of potential long-term isolation hampers effective management efforts. In the present study, we reconstructed the seahorses’ demographic history using a suite of microsatellite loci. We found that the largest population (Knysna Estuary) has colonised the other estuaries relatively recently (< 450 years ago), and that its population size is comparatively large and stable. Neither of the other two populations shows signs of long-term reductions in population size. The high conservation status of the species is thus a result of its limited range rather than historical population declines. Our findings indicate that the long-term survival of H. capensis depends primarily on the successful management of the Knysna population, although the other estuaries may serve as reservoirs of genetic diversity.

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Low diversity, little genetic structure but no inbreeding in a high density island endemic pit-viper Gloydius shedaoensis

Current Zoology ◽

10.1093/cz/zoab084 ◽

2021 ◽

Author(s):

Guannan Wen ◽

Long Jin ◽

Yayong Wu ◽

Xiaoping Wang ◽

Jinzhong Fu ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Population Size ◽

Demographic History ◽

Iucn Red List ◽

Conservation Priorities ◽

Important Species ◽

Island Endemic ◽

Island Species ◽

Low Genetic Diversity

Abstract Islands species and their ecosystems play an important role in global biodiversity preservation, and many vulnerable island species are conservation priorities. Although insular habitat likely facilitates the species diversification process, it may also aggravate the fragility of these species with high risk of inbreeding. The Shedao pit-viper Gloydius shedaoensis is an island endemic species with an extremely high population density, which has been categorized as vulnerable in the IUCN Red List. We collected 13,148 SNP from across its genome and examined its genetic diversity and demographic history. The Shedao pit-viper has a low genetic diversity but shows no sign of inbreeding. Furthermore, population genetic structure analysis, including the NJ tree, PCoA, clustering, and spatial autocorrelation, revealed a general lack of spatial structure. Only the IBD residues suggested a weak patchiness. Overall, the population is nearly panmictic and gene flow is evenly distributed across the island. The large number of individuals, small size of the island, and the lack of population structure likely all contribute to the lack of inbreeding in this species. We also detected signs of male-biased dispersal, which likely is another inbreeding avoidance strategy. Historical demographic analysis suggested that the historical population size and distribution of the species are much larger than their current ones. The multiple transgressive-regressive events since the Late Pleistocene are likely the main cause of the population size changes. Taken together, our results provide a basic scientific foundation for the conservation of this interesting and important species.

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Genetic Diversity, Inbreeding Level, and Genetic Load in Endangered Snub-Nosed Monkeys (Rhinopithecus)

Frontiers in Genetics ◽

10.3389/fgene.2020.615926 ◽

2020 ◽

Vol 11 ◽

Author(s):

Weimin Kuang ◽

Jingyang Hu ◽

Hong Wu ◽

Xiaotian Fen ◽

Qingyan Dai ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Large Population ◽

Population Decline ◽

Genetic Load ◽

Term Survival ◽

Population Sizes ◽

Genomic Inbreeding ◽

Inbreeding Level

The snub-nosed monkey genus (Rhinopithecus) comprises five closely related species (R. avunculus, R. bieti, R. brelichi, R. roxellana, and R. strykeri). All are among the world's rarest and most endangered primates. However, the genomic impact associated with their population decline remains unknown. We analyzed population genomic data of all five snub-nosed monkey species to assess their genetic diversity, inbreeding level, and genetic load. For R. roxellana, R. bieti, and R. strykeri, population size is positively correlated with genetic diversity and negatively correlated with levels of inbreeding. Other species, however, which possess small population sizes, such as R. brelichi and R. avunculus, show high levels of genetic diversity and low levels of genomic inbreeding. Similarly, in the three populations of R. roxellana, the Shennongjia population, which possesses the lowest population size, displays a higher level of genetic diversity and lower level of genomic inbreeding. These findings suggest that although R. brelichi and R. avunculus and the Shennongjia population might be at risk, it possess significant genetic diversity and could thus help strengthen their long-term survival potential. Intriguingly, R. roxellana with large population size possess high genetic diversity and low level of genetic load, but they show the highest recent inbreeding level compared with the other snub-nosed monkeys. This suggests that, despite its large population size, R. roxellana has likely been experiencing recent inbreeding, which has not yet affected its mutational load and fitness. Analyses of homozygous-derived deleterious mutations identified in all snub-nosed monkey species indicate that these mutations are affecting immune, especially in smaller population sizes, indicating that the long-term consequences of inbreeding may be resulting in an overall reduction of immune capability in the snub-nosed monkeys, which could provide a dramatic effect on their long-term survival prospects. Altogether, our study provides valuable information concerning the genomic impact of population decline of the snub-nosed monkeys. We revealed multiple counterintuitive and unexpected patterns of genetic diversity in small and large population, which will be essential for conservation management of these endangered species.

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Impacts of the Toba eruption and montane forest expansion on diversification in Sumatran parachuting frogs (Rhacophorus)

10.1101/843664 ◽

2019 ◽

Author(s):

Kyle A. O’Connell ◽

Jamie R. Oaks ◽

Amir Hamidy ◽

Kyle J. Shaney ◽

Nia Kurniawan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Demographic History ◽

Volcanic Eruptions ◽

Population Declines ◽

Effective Population ◽

Size Change ◽

Forest Expansion ◽

Target Capture ◽

Full Likelihood

Catastrophic events, such as volcanic eruptions, can have profound impacts on the demographic histories of resident taxa. Due to its presumed effect on biodiversity, the Pleistocene eruption of super-volcano Toba has received abundant attention. We test the effects of the Toba eruption on the diversification, genetic diversity, and demography of three co-distributed species of parachuting frogs (Genus Rhacophorus) on Sumatra. We generate target-capture data (∼950 loci and ∼440,000 bp) for three species of parachuting frogs and use these data paired with previously generated double digest restriction-site associated DNA (ddRADseq) data to estimate population structure and genetic diversity, to test for population size changes using demographic modelling, and to estimate the temporal clustering of size change events using a full-likelihood Bayesian method. We find that populations around Toba exhibit reduced genetic diversity compared with southern populations, and that northern populations exhibit a shift in effective population size around the time of the eruption (∼80 kya). However, we infer a stronger signal of expansion in southern populations around ∼400 kya, and at least two of the northern populations may have also expanded at this time. Taken together, these findings suggest that the Toba eruption precipitated population declines in northern populations, but that the demographic history of these three species was also strongly impacted by mid-Pleistocene forest expansion during glacial periods. We propose local rather than regional effects of the Toba eruption, and emphasize the dynamic nature of diversification on the Sunda Shelf.

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Demographic decline and lineage-specific adaptations characterize New Zealand kiwi

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.2362 ◽

2021 ◽

Vol 288 (1965) ◽

Author(s):

Jordan B. Bemmels ◽

Else K. Mikkelsen ◽

Oliver Haddrath ◽

Rogan M. Colbourne ◽

Hugh A. Robertson ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Population Size ◽

Genetic Drift ◽

Demographic History ◽

Small Population ◽

Population Declines ◽

Demographic Stochasticity ◽

Fragmented Populations ◽

Low Genetic Diversity

Small and fragmented populations may become rapidly differentiated due to genetic drift, making it difficult to distinguish whether neutral genetic structure is a signature of recent demographic events, or of long-term evolutionary processes that could have allowed populations to adaptively diverge. We sequenced 52 whole genomes to examine Holocene demographic history and patterns of adaptation in kiwi ( Apteryx ), and recovered 11 strongly differentiated genetic clusters corresponding to previously recognized lineages. Demographic models suggest that all 11 lineages experienced dramatic population crashes relative to early- or mid-Holocene levels. Small population size is associated with low genetic diversity and elevated genetic differentiation ( F ST ), suggesting that population declines have strengthened genetic structure and led to the loss of genetic diversity. However, population size is not correlated with inbreeding rates. Eight lineages show signatures of lineage-specific selective sweeps (284 sweeps total) that are unlikely to have been caused by demographic stochasticity. Overall, these results suggest that despite strong genetic drift associated with recent bottlenecks, most kiwi lineages possess unique adaptations and should be recognized as separate adaptive units in conservation contexts. Our work highlights how whole-genome datasets can address longstanding uncertainty about the evolutionary and conservation significance of small and fragmented populations of threatened species.

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Dramatic decline of François' langur Trachypithecus francoisi in Guangxi Province, China

Oryx ◽

10.1017/s0030605307001500 ◽

2007 ◽

Vol 41 (1) ◽

pp. 38-43 ◽

Cited By ~ 24

Author(s):

Youbang Li ◽

Chengming Huang ◽

Ping Ding ◽

Zheng Tang ◽

Chris Wood

Keyword(s):

Population Size ◽

Conservation Status ◽

Guangxi Province ◽

Isolated Populations ◽

Term Survival ◽

Management Planning ◽

Management Measures ◽

Species Survival ◽

Dramatic Decline ◽

Trachypithecus Francoisi

Interviews with local people and a survey were carried out in 23 counties of south-west Guangxi Province from April 2002 to June 2003 to evaluate the conservation status of François' langur Trachypithecus francoisi and assess the extent and nature of threats to the species' survival. François' langurs were found in only 10 counties compared with their presence in 23 counties before 1990. The total population size is estimated to be 307 individuals in 14 isolated populations. This represents a 90% decrease in population size since the early 1980s and an 85% decrease since the mid 1990s. The primary threat to the langur is hunting, mainly for traditional medicine. Our results suggest that conservation efforts for the species have been ineffectual during the last decade and, even within reserves, few direct management measures seem to have been taken to protect and conserve the langurs. Without the instigation of such measures it seems likely that François' langur will disappear both inside and outside reserves. To ensure the long-term survival of Francois' langur in Guangxi Province increased investment and improved management, planning, and training of reserve managers and staff is required, with a particular focus on the key remaining reserves and sites for the langur. Some of this work is now underway.

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Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2019.2613 ◽

2020 ◽

Vol 287 (1922) ◽

pp. 20192613 ◽

Cited By ~ 2

Author(s):

Elisa G. Dierickx ◽

Simon Yung Wa Sin ◽

H. Pieter J. van Veelen ◽

M. de L. Brooke ◽

Yang Liu ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Sex Chromosomes ◽

Demographic History ◽

Large Population ◽

Effective Population ◽

Island Species ◽

Population Sizes ◽

Approaches To Study ◽

Genetic Signatures

Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events.

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Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽

10.3390/ani9060361 ◽

2019 ◽

Vol 9 (6) ◽

pp. 361 ◽

Cited By ~ 3

Author(s):

Shuqi Diao ◽

Shuwen Huang ◽

Zhiting Xu ◽

Shaopan Ye ◽

Xiaolong Yuan ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Conservation Status ◽

Snp Array ◽

Size Analysis ◽

Selection Signatures ◽

Effective Population ◽

Low Genetic Diversity ◽

Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

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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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Corporate culture and long-term survival of Spanish innovative firms

International Journal of Innovation Science ◽

10.1108/ijis-11-2016-0053 ◽

2017 ◽

Vol 9 (4) ◽

pp. 335-354 ◽

Cited By ~ 4

Author(s):

Manuel Ramón Tejeiro Koller ◽

Patricio Morcillo Ortega ◽

José Miguel Rodríguez Antón ◽

Luís Rubio Andrada

Keyword(s):

Corporate Culture ◽

Business Environment ◽

The Other ◽

Management Tool ◽

Term Survival ◽

Content Type ◽

Innovation Culture ◽

Innovative Firms ◽

Innovative Capabilities

Purpose The purpose of this paper is to analyze how firms can enhance their innovative capabilities and become more resilient. The current business environment requires a specific type of management for companies to remain competitive and innovation plays a key role in this respect. However, this means that a particular kind of corporate culture must promote innovation in the firm. This innovation culture is likely to be present in innovative companies that have survived in the long term (at least 50 years) and be the source of an adaptive advantage. Design/methodology/approach Using innovative Spanish firms, which were established at least 50 years ago, an exploratory factorial analysis was conducted to verify the existence of an innovation culture. Thereafter, a cluster analysis was undertaken to study differences in performance to be able to detect and identify their adaptive advantage. Findings The findings offer a detailed profile of old and innovative firms created in Spain. Results show that most of the studied firms (88 per cent) have an innovation culture. Furthermore, two separate groups were identified, in which one showed higher profitability and a lower adjustment to an innovation culture, while the other showed the reverse results. This suggests that innovation culture helps companies be more resilient but does not necessarily lead to higher returns. Practical implications Corporate culture is identified as a useful management tool in the search for more resilient enterprises. Specific cultural traits are recommended and a benchmarking tool is applied and made available upon request. Originality/value Although there are a number of studies which consider the concept of adaptive advantage and resilience on the one side, and on corporate innovation culture on the other, this paper seems to be the first to empirically explore the relationship of both these concepts.

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