A tale of two forests: ongoing aridification drives population decline and genetic diversity loss at continental scale in Afro-Macaronesian evergreen-forest archipelago endemics

AbstractThe gharial (Gavialis gangeticus) is a critically endangered crocodylian, endemic to the Indian subcontinent. The species has experienced severe population decline during the twentieth century owing to habitat loss, poaching, and mortalities in passive fishing. Its extant populations have largely recovered through translocation programmes initiated in 1975. Understanding the genetic status of these populations is crucial for evaluating the effectiveness of the ongoing conservation efforts. This study assessed the genetic diversity, population structure, and evidence of genetic bottlenecks of the two managed populations inhabiting the Chambal and Girwa Rivers, which hold nearly 80% of the global gharial populations. We used seven polymorphic nuclear microsatellite loci and a 520 bp partial fragment of the mitochondrial control region (CR). The overall mean allelic richness (Ar) was 2.80 ± 0.40, and the observed (Ho) and expected (He) heterozygosities were 0.40 ± 0.05 and 0.39 ± 0.05, respectively. We observed low levels of genetic differentiation between populations (FST = 0.039, P < 0.05; G’ST = 0.058, P < 0.05 Jost’s D = 0.016, P < 0.05). The bottleneck analysis using the M ratio (Chambal = 0.31 ± 0.06; Girwa = 0.41 ± 0.12) suggested the presence of a genetic bottleneck in both populations. The mitochondrial CR also showed a low level of variation, with two haplotypes observed in the Girwa population. This study highlights the low level of genetic diversity in the two largest managed gharial populations in the wild. Hence, it is recommended to assess the genetic status of extant wild and captive gharial populations for planning future translocation programmes to ensure long-term survival in the wild.

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Large numbers of vertebrates began rapid population decline in the late 19th century

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1616804113 ◽

2016 ◽

Vol 113 (49) ◽

pp. 14079-14084 ◽

Cited By ~ 20

Author(s):

Haipeng Li ◽

Jinggong Xiang-Yu ◽

Guangyi Dai ◽

Zhili Gu ◽

Chen Ming ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Threatened Species ◽

Driving Forces ◽

Population Decline ◽

Cumulative Effect ◽

Extinction Time ◽

Time Period ◽

Large Numbers ◽

The Difference

Accelerated losses of biodiversity are a hallmark of the current era. Large declines of population size have been widely observed and currently 22,176 species are threatened by extinction. The time at which a threatened species began rapid population decline (RPD) and the rate of RPD provide important clues about the driving forces of population decline and anticipated extinction time. However, these parameters remain unknown for the vast majority of threatened species. Here we analyzed the genetic diversity data of nuclear and mitochondrial loci of 2,764 vertebrate species and found that the mean genetic diversity is lower in threatened species than in related nonthreatened species. Our coalescence-based modeling suggests that in many threatened species the RPD began ∼123 y ago (a 95% confidence interval of 20–260 y). This estimated date coincides with widespread industrialization and a profound change in global living ecosystems over the past two centuries. On average the population size declined by ∼25% every 10 y in a threatened species, and the population size was reduced to ∼5% of its ancestral size. Moreover, the ancestral size of threatened species was, on average, ∼22% smaller than that of nonthreatened species. Because the time period of RPD is short, the cumulative effect of RPD on genetic diversity is still not strong, so that the smaller ancestral size of threatened species may be the major cause of their reduced genetic diversity; RPD explains 24.1–37.5% of the difference in genetic diversity between threatened and nonthreatened species.

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Climate Warming as a Possible Trigger of Keystone Mussel Population Decline in Oligotrophic Rivers at the Continental Scale

Scientific Reports ◽

10.1038/s41598-017-18873-y ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 18

Author(s):

Ivan N. Bolotov ◽

Alexander A. Makhrov ◽

Mikhail Yu. Gofarov ◽

Olga V. Aksenova ◽

Paul E. Aspholm ◽

...

Keyword(s):

Climate Warming ◽

Population Decline ◽

Mussel Population ◽

Continental Scale

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Genetic Diversity of the Cestode Echinococcus multilocularis in Red Foxes at a Continental Scale in Europe

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0000452 ◽

2009 ◽

Vol 3 (6) ◽

pp. e452 ◽

Cited By ~ 43

Author(s):

Jenny Knapp ◽

Jean-Mathieu Bart ◽

Patrick Giraudoux ◽

Marie-Louise Glowatzki ◽

Isabelle Breyer ◽

...

Keyword(s):

Genetic Diversity ◽

Echinococcus Multilocularis ◽

Red Foxes ◽

Continental Scale

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Challenges to assessing connectivity between massive populations of the Australian plague locust

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.2605 ◽

2011 ◽

Vol 278 (1721) ◽

pp. 3152-3160 ◽

Cited By ~ 24

Author(s):

Marie-Pierre Chapuis ◽

Julie-Anne M. Popple ◽

Karine Berthier ◽

Stephen J. Simpson ◽

Edward Deveson ◽

...

Keyword(s):

Genetic Diversity ◽

Large Population ◽

Movement Ecology ◽

Effective Population ◽

Continental Scale ◽

Australian Continent ◽

Population Structuring ◽

Population Sizes ◽

Approximate Bayesian ◽

Australian Plague Locust

Linking demographic and genetic dispersal measures is of fundamental importance for movement ecology and evolution. However, such integration can be difficult, particularly for highly fecund species that are often the target of management decisions guided by an understanding of population movement. Here, we present an example of how the influence of large population sizes can preclude genetic approaches from assessing demographic population structuring, even at a continental scale. The Australian plague locust, Chortoicetes terminifera , is a significant pest, with populations on the eastern and western sides of Australia having been monitored and managed independently to date. We used microsatellites to assess genetic variation in 12 C. terminifera population samples separated by up to 3000 km. Traditional summary statistics indicated high levels of genetic diversity and a surprising lack of population structure across the entire range. An approximate Bayesian computation treatment indicated that levels of genetic diversity in C. terminifera corresponded to effective population sizes conservatively composed of tens of thousands to several million individuals. We used these estimates and computer simulations to estimate the minimum rate of dispersal, m , that could account for the observed range-wide genetic homogeneity. The rate of dispersal between both sides of the Australian continent could be several orders of magnitude lower than that typically considered as required for the demographic connectivity of populations.

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Population decline in semi-migratory caribou (Rangifer tarandus): intrinsic or extrinsic drivers?

Canadian Journal of Zoology ◽

10.1139/cjz-2013-0154 ◽

2013 ◽

Vol 91 (11) ◽

pp. 820-828 ◽

Cited By ~ 15

Author(s):

Guillaume Bastille-Rousseau ◽

James A. Schaefer ◽

Shane P. Mahoney ◽

Dennis L. Murray

Keyword(s):

Density Dependence ◽

Rangifer Tarandus ◽

Vegetation Index ◽

Normalized Difference Vegetation Index ◽

Population Decline ◽

Negative Relationship ◽

Population Limitation ◽

Continental Scale ◽

Delayed Density Dependence ◽

Winter Severity

Many populations of caribou (Rangifer tarandus (L., 1758)) across North America, including Newfoundland, are in a state of decline. This phenomenon may reflect continental-scale changes in either the extrinsic or the intrinsic factors affecting caribou abundance. We hypothesized that caribou decline reflected marked resource limitation and predicted that fluctuations should correspond to time-delayed density dependence associated with a decline in range quality and decadal trends in winter severity. By conducting time-series analysis using 12 populations and evaluating correlations between caribou abundance and trends in (i) vegetation available at calving (normalized difference vegetation index, NDVI), (ii) winter weather severity (index of North Atlantic Oscillation, NAO), and (iii) caribou morphometrics, we observed strong evidence of density dependence in population dynamics (i.e., a negative relationship between caribou population size and caribou morphometrics). Caribou population trajectories were time-delayed relative to winter severity, but not relative to calving-ground greenness. These island-wide correlations could not be traced to dispersal between herds, which appears rare at least for adult females. Our results suggest that trends in winter severity may synchronize broad-scale changes in caribou abundance that are driven by time-delayed density dependence, although it remains possible that calving-ground deterioration also may contribute to population limitation in Newfoundland. Our findings provide the basis for additional research into density dependence and caribou population decline.

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Population connectivity buffers genetic diversity loss in a seabird

Frontiers in Zoology ◽

10.1186/1742-9994-10-28 ◽

2013 ◽

Vol 10 (1) ◽

pp. 28 ◽

Cited By ~ 13

Author(s):

Oscar Ramírez ◽

Elena Gómez-Díaz ◽

Iñigo Olalde ◽

Juan Illera ◽

Juan Rando ◽

...

Keyword(s):

Genetic Diversity ◽

Population Connectivity ◽

Diversity Loss

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Population decline is accompanied by loss of genetic diversity in the Lesser Grey Shrike Lanius minor

Ibis ◽

10.1111/j.1474-919x.2010.01091.x ◽

2010 ◽

Vol 153 (1) ◽

pp. 98-109 ◽

Cited By ~ 5

Author(s):

LAURA KVIST ◽

DAVID GIRALT ◽

FRANCISCO VALERA ◽

HERBERT HOI ◽

ANTON KRISTIN ◽

...

Keyword(s):

Genetic Diversity ◽

Population Decline ◽

Lesser Grey Shrike ◽

Loss Of Genetic Diversity ◽

Grey Shrike

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Nuclear and cytoplasmic genetic diversity reveals long-term population decline in Abies semenovii, an endemic fir of central Asia

Canadian Journal of Forest Research ◽

10.1139/cjfr-2012-0158 ◽

2012 ◽

Vol 42 (12) ◽

pp. 2142-2152 ◽

Cited By ~ 5

Author(s):

Svetlana A. Semerikova ◽

Martin Lascoux ◽

Vladimir L. Semerikov

Keyword(s):

Genetic Diversity ◽

Central Asia ◽

Population Decline ◽

Population Expansion ◽

Nuclear Marker ◽

Effective Population ◽

Species Status ◽

Siberian Fir ◽

Low Genetic Diversity

The genus Abies is one of the largest conifer genera and many of the marginal species remain poorly characterized. Abies semenovii B. Fedtsch. is a rare mountain fir species from central Asia, and its species status is still disputed. We used both nuclear (allozymes and AFLP) and chloroplastic (cpSSR) markers to show that A. semenovii deserves to be considered as a species and that its low genetic diversity justifies more a proactive conservation policy. First, A. semenovii was significantly differentiated from the Siberian fir Abies sibirica Ledeb. and we did not detect gene flow between the two species. Second, A. semenovii has a very low nuclear genetic diversity, suggesting a prolonged restricted effective population size. Abies semenovii had low cpSSR diversity too but the identification of seven closely related haplotypes suggests that these mutations accumulated recently during a phase of population expansion. This agrees well with the palynological record and is in contrast with the situation observed in another rare Eurasian fir endemic to Kamchatka, Abies gracilis Kom., which was devoid of variation in cpSSRs but that also had a more substantial nuclear marker diversity than A. semenovii, thereby suggesting a more recent but less severe population bottleneck.

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Phylogenetic Diversity of Koala Retrovirus within a Wild Koala Population

Journal of Virology ◽

10.1128/jvi.01820-16 ◽

2016 ◽

Vol 91 (3) ◽

Cited By ~ 23

Author(s):

K. J. Chappell ◽

J. C. Brealey ◽

A. A. Amarilla ◽

D. Watterson ◽

L. Hulse ◽

...

Keyword(s):

Genetic Diversity ◽

Phylogenetic Diversity ◽

Germ Line ◽

Population Decline ◽

Hypervariable Region ◽

Sequence Divergence ◽

The United States ◽

High Prevalence ◽

Amino Acid Sequence Divergence ◽

Koala Retrovirus

ABSTRACT Koala populations are in serious decline across many areas of mainland Australia, with infectious disease a contributing factor. Koala retrovirus (KoRV) is a gammaretrovirus present in most wild koala populations and captive colonies. Five subtypes of KoRV (A to E) have been identified based on amino acid sequence divergence in a hypervariable region of the receptor binding domain of the envelope protein. However, analysis of viral genetic diversity has been conducted primarily on KoRV in captive koalas housed in zoos in Japan, the United States, and Germany. Wild koalas within Australia have not been comparably assessed. Here we report a detailed analysis of KoRV genetic diversity in samples collected from 18 wild koalas from southeast Queensland. By employing deep sequencing we identified 108 novel KoRV envelope sequences and determined their phylogenetic diversity. Genetic diversity in KoRV was abundant and fell into three major groups; two comprised the previously identified subtypes A and B, while the third contained the remaining hypervariable region subtypes (C, D, and E) as well as four hypervariable region subtypes that we newly define here (F, G, H, and I). In addition to the ubiquitous presence of KoRV-A, which may represent an exclusively endogenous variant, subtypes B, D, and F were found to be at high prevalence, while subtypes G, H, and I were present in a smaller number of animals. IMPORTANCE Koala retrovirus (KoRV) is thought to be a significant contributor to koala disease and population decline across mainland Australia. This study is the first to determine KoRV subtype prevalence among a wild koala population, and it significantly expands the total number of KoRV sequences available, providing a more precise picture of genetic diversity. This understanding of KoRV subtype prevalence and genetic diversity will be important for conservation efforts attempting to limit the spread of KoRV. Furthermore, KoRV is one of the only retroviruses shown to exist in both endogenous (transmitted vertically to offspring in the germ line DNA) and exogenous (horizontally transmitted between infected individuals) forms, a division of fundamental evolutionary importance.

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