Effects of habitat fragmentation, population size and demographic history on genetic diversity: the cross river gorilla in a comparative context

Abstract Taxus yunnanensis, which is an endangered tree that is considered valuable because it contains the effective natural anticancer metabolite taxol and heteropolysaccharides, has long suffered from severe habitat fragmentation. In this study, the levels of genetic diversity in two populations of 136 individuals were analyzed based on eleven polymorphic microsatellite loci. Our results suggested that these two populations were characterized by low genetic diversity (NE = 2.303/2.557; HO = 0.168/0.142; HE = 0.453/0.517), a population bottleneck, a low effective population size (Ne = 7/9), a high level of inbreeding (FIS = 0.596/0.702), and a weak, but significant spatial genetic structure (Sp = 0.001, b = −0.001*). Habitat fragmentation, seed shadow overlap and limited seed and pollen dispersal and potential selfing may have contributed to the observed gene tic structure. The results of the present study will enable development of practical conservation measures to effectively conserve the valuable genetic resources of this endangered plant.

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Nest site ecology of the cross river gorilla at the Kagwene Gorilla Sanctuary, Cameroon, with special reference to anthropogenic influence

American Journal of Primatology ◽

10.1002/ajp.20886 ◽

2010 ◽

Vol 73 (3) ◽

pp. 253-261 ◽

Cited By ~ 8

Author(s):

Ruth A. De Vere ◽

Ymke Warren ◽

Aaron Nicholas ◽

Mary E. Mackenzie ◽

James P. Higham

Keyword(s):

Special Reference ◽

Nest Site ◽

Anthropogenic Influence ◽

Cross River ◽

Cross River Gorilla ◽

The Cross ◽

Site Ecology

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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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The Cross River gorilla: Natural history and status of a neglected and critically endangered subspecies

Gorilla Biology ◽

10.1017/cbo9780511542558.021 ◽

2002 ◽

pp. 472-497 ◽

Cited By ~ 2

Author(s):

John F. Oates ◽

Kelley L. McFarland ◽

Jaqueline L. Groves ◽

Richard A. Bergl ◽

Joshua M. Linder ◽

...

Keyword(s):

Natural History ◽

Critically Endangered ◽

Cross River ◽

Cross River Gorilla ◽

The Cross

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Low Neutral Genetic Diversity in an Isolated Greater Sage Grouse (Centrocercus Urophasianus) Population in Northwest Wyoming

The UW National Parks Service Research Station Annual Reports ◽

10.13001/uwnpsrc.2012.3943 ◽

2012 ◽

Vol 35 ◽

pp. 119-133

Author(s):

Sarah Schulwitz ◽

Jeff Johnson ◽

Bryan Bedrosian

Keyword(s):

Genetic Diversity ◽

Habitat Fragmentation ◽

Population Size ◽

Centrocercus Urophasianus ◽

Small Population ◽

Suitable Habitat ◽

Sage Grouse ◽

Asymmetric Dispersal ◽

Anthropogenic Habitat ◽

Neutral Genetic Diversity

Habitat loss is well recognized as an immediate threat to biodiversity. Depending on the dispersal capabilities of the species, increased habitat fragmentation often results in reduced functional connectivity and gene flow followed by population decline and a higher likelihood of eventual extinction. Knowledge of the degree of connectivity between populations is therefore crucial for better management of small populations in a changing landscape. A small population of greater sage-grouse (Centrocercus urophasianus) exists in northwest Wyoming within the Jackson Hole valley, including Grand Teton National Park and the National Elk Refuge. To what degree the Jackson population is isolated is not known as natural dispersal barriers in the form of mountains and anthropogenic habitat fragmentation may limit the populationâs connectivity to adjacent populations. Using 16 microsatellite loci and 300 greater sage-grouse samples collected throughout Wyoming and southeast Montana, significant population differentiation was found to exist among populations. Results indicated that the Jackson population was isolated relative to the other sampled populations, including Pinedale, its closest neighboring large population to the south. The one exception was a small population immediately to the east of Jackson, in which asymmetric dispersal from Jackson into Gros Ventre was detected. Both Jackson and Gros Ventre populations exhibited significantly reduced levels of neutral genetic diversity relative to other sampled populations. More work is warranted to determine the timing at which Jackson and Gros Ventre populations had become isolated and whether it was primarily due to recent habitat fragmentation or more historic processes. Due to its small population size, continual monitoring of the population is recommended with the goal of at least maintaining current population size and, if possible, increasing suitable habitat and population size to levels recorded in the past.

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Effects of habitat fragmentation and human disturbance on the population dynamics of the Yunnan snub-nosed monkey from 1994 to 2016

PeerJ ◽

10.7717/peerj.6633 ◽

2019 ◽

Vol 7 ◽

pp. e6633 ◽

Cited By ~ 5

Author(s):

Xumao Zhao ◽

Baoping Ren ◽

Dayong Li ◽

Zuofu Xiang ◽

Paul A. Garber ◽

...

Keyword(s):

Genetic Diversity ◽

Population Dynamics ◽

Habitat Fragmentation ◽

Population Size ◽

Linear Models ◽

Conservation Strategies ◽

Source Population ◽

Forest Patches ◽

Current Conservation ◽

Conservation Policies

In this study, we integrate data from field investigations, spatial analysis, genetic analysis, and Generalized Linear Models (GLMs) to evaluate the effects of habitat fragmentation on the population dynamics, genetic diversity, and range shifts in the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti). The results indicate that from 1994 to 2016, R. bieti population size increased from less than 2,000 to approximately 3,000 individuals. A primary factor promoting population recovery was the establishment of protected nature reserves. We also found that subpopulation growth rates were uneven, with the groups in some areas, and the formation of new groups. Both the fragmentation index, defined as the ratio of the number of forest patches to the total area of forest patches (e.g., increased fragmentation), and increasing human population size had a negative effect on population growth in R. bieti. We recommend that government conservation plans prioritize the protection of particular R. bieti populations, such as the Baimei and Jisichang populations, which have uncommon haplotypes. In addition, effective conservation strategies need to include an expansion of migration corridors to enable individuals from larger populations such as Guyoulong (Guilong) to serve as a source population to increase the genetic diversity of smaller R. bieti subpopulations. We argue that policies designed to protect endangered primates should not focus solely on total population size but also need to determine the amount of genetic diversity present across different subpopulations and use this information as a measure of the effectiveness of current conservation policies and the basis for new conservation policies.

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Demography and natural selection have shaped genome-wide variation in the widely distributed conifer Norway Spruce (Picea abies)

10.1101/805903 ◽

2019 ◽

Author(s):

Xi Wang ◽

Carolina Bernhardsson ◽

Pär K. Ingvarsson

Keyword(s):

Genetic Diversity ◽

Natural Selection ◽

Picea Abies ◽

Population Size ◽

Effective Population Size ◽

Norway Spruce ◽

Demographic History ◽

Sequencing Data ◽

Effective Population ◽

Genome Wide

AbstractUnder the neutral theory, species with larger effective population sizes are expected to harbour higher genetic diversity. However, across a wide variety of organisms, the range of genetic diversity is orders of magnitude more narrow than the range of effective population size. This observation has become known as Lewontin’s paradox and although aspects of this phenomenon have been extensively studied, the underlying causes for the paradox remain unclear. Norway spruce (Picea abies) is a widely distributed conifer species across the northern hemisphere and it consequently plays a major role in European forestry. Here, we use whole-genome re-sequencing data from 35 individuals to perform population genomic analyses in P. abies in an effort to understand what drives genome-wide patterns of variation in this species. Despite having a very wide geographic distribution and an enormous current population size, our analyses find that genetic diversity of P.abies is low across a number of populations (p=0.005-0.006). To assess the reasons for the low levels of genetic diversity, we infer the demographic history of the species and find that it is characterised by several re-occurring bottlenecks with concomitant decreases in effective population size can, at least partly, provide an explanation for low polymorphism we observe in P. abies. Further analyses suggest that recurrent natural selection, both purifying and positive selection, can also contribute to the loss of genetic diversity in Norway spruce by reducing genetic diversity at linked sites. Finally, the overall low mutation rates seen in conifers can also help explain the low genetic diversity maintained in Norway spruce.

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Genetic consequences of subtropical rainforest fragmentation on Macadamia tetraphylla (Proteaceae)

Silvae Genetica ◽

10.1515/sg-2011-0032 ◽

2011 ◽

Vol 60 (1-6) ◽

pp. 241-249 ◽

Cited By ~ 6

Author(s):

C. S. Spain ◽

A. J. Lowe

Keyword(s):

Genetic Diversity ◽

Habitat Fragmentation ◽

Population Size ◽

Population Differentiation ◽

Adult Population ◽

Population Divergence ◽

Population Bottlenecks ◽

Significant Difference ◽

Adult Tree ◽

Eventual Loss

Abstract Habitat fragmentation can bring about a variety of gene-flow alterations in plant populations, potentially threatening adaptive potential and local persistence. It is expected that following habitat fragmentation an increased level of inbreeding will be evident. In addition, a reduction in genetic diversity and increased genetic differentiation is expected following severe or long term population bottlenecks. We examined population genetic parameters for the subtropical rainforest tree Macadamia tetraphylla (Proteaceae) at six field sites throughout its recently fragmented range, using four microsatellite loci. Genetic diversity (HE) of the juvenile cohort was significantly correlated with estimated population size. No significant difference was observed for genetic diversity between adult and juvenile cohorts, but juveniles, and not adults, exhibited significant population differentiation (θ =0.061; P<0.0001 and θ =0.016; P=0.23, respectively). A second, standardised measure of differentiation, ×′, yielded similarly large differences between the two cohorts, though higher estimates of differentiation overall (adults – θ′=0.034, juveniles – θ′=0.116). The coefficient of population inbreeding (f) was significant and positive in all juvenile, and four out of six adult, populations, and was significantly positively correlated with adult tree density, but not adult population size. Since fragmentation is relatively recent for this species, the population bottleneck must have been quite severe to have produced the observed patterns of population differentiation and genetic diversity. Fragmentation of forest across the study area over the last 100+ years has led to the genetic isolation of M. tetraphylla populations resulting in increased population divergence and likely eventual loss of genetic variation in future generations.

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

Scientific Reports ◽

10.1038/s41598-021-83754-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Thomas Kalama Mkare ◽

Bettine Jansen van Vuuren ◽

Peter R. Teske

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Demographic History ◽

Conservation Status ◽

Limited Range ◽

The Other ◽

Conservation Priorities ◽

Population Declines ◽

Term Survival

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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