Causes of hatching failure in endangered birds

Hemmings, Nicola; West, Matt; Birkhead, Tim R.

doi:10.1098/rsbl.2012.0655

Cited by 35 publications

(50 citation statements)

References 30 publications

(42 reference statements)

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“…In fact, even under the perception of relatively ideal biological conditions in the field, N e for large K -selected avian species like the scarlet macaw may be much lower than presumed based on the amount of available habitat, and the estimated total population size. Our findings highlight the need to conserve large populations of scarlet macaws and similar species in order to maintain genomic diversity and corresponding N e to avoid unmasking deleterious alleles by way of increasing homozygosity, as observed for the highly endangered Spix's Macaws [75]–[76]. However, caution is necessary when interpreting the results of PSMC, as population size reductions and population fragmentation may not always be easily differentiated [55].…”

Section: Resultsmentioning

confidence: 68%

A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene

Halley

Dowd²,

Decker

et al. 2014

PLoS ONE

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Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within <40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for >14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the scarlet macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts.

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Section: Resultsmentioning

confidence: 68%

A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene

Halley

Dowd²,

Decker

et al. 2014

PLoS ONE

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“…The single generation of sibling mating performed here represents strong inbreeding, but even in natural populations, inbreeding can sometimes be quite intense (Keller & Waller, ). Lower rates of nonrandom mating found in captive populations could purge deleterious alleles (Glémin, ), nonetheless captive population often exhibit inbreeding depression rather than purging (Hemmings et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Role of propagule pressure in colonization success: disentangling the relative importance of demographic, genetic and habitat effects

Hufbauer

Rutschmann

Serrate

et al. 2013

J of Evolutionary Biology

105

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High propagule pressure is arguably the only consistent predictor of colonization success. More individuals enhance colonization success because they aid in overcoming demographic consequences of small population size (e.g. stochasticity and Allee effects). The number of founders can also have direct genetic effects: with fewer individuals, more inbreeding and thus inbreeding depression will occur, whereas more individuals typically harbour greater genetic variation. Thus, the demographic and genetic components of propagule pressure are interrelated, making it difficult to understand which mechanisms are most important in determining colonization success. We experimentally disentangled the demographic and genetic components of propagule pressure by manipulating the number of founders (fewer or more), and genetic background (inbred or outbred) of individuals released in a series of three complementary experiments. We used Bemisia whiteflies and released them onto either their natal host (benign) or a novel host (challenging). Our experiments revealed that having more founding individuals and those individuals being outbred both increased the number of adults produced, but that only genetic background consistently shaped net reproductive rate of experimental populations. Environment was also important and interacted with propagule size to determine the number of adults produced. Quality of the environment interacted also with genetic background to determine establishment success, with a more pronounced effect of inbreeding depression in harsh environments. This interaction did not hold for the net reproductive rate. These data show that the positive effect of propagule pressure on founding success can be driven as much by underlying genetic processes as by demographics. Genetic effects can be immediate and have sizable effects on fitness.

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“…Data on inbreeding depression in cassidix are very limited, although some evidence of lower egg fertility in captive, relative to wild, cassidix has previously been reported (6/19 captive eggs were infertile, whereas none of a small sample of four wild eggs were infertile; Hemmings et al . ).…”

Section: Introductionmentioning

confidence: 97%

Scope for genetic rescue of an endangered subspecies though re‐establishing natural gene flow with another subspecies

et al. 2016

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Genetic diversity is positively linked to the viability and evolutionary potential of species but is often compromised in threatened taxa. Genetic rescue by gene flow from a more diverse or differentiated source population of the same species can be an effective strategy for alleviating inbreeding depression and boosting evolutionary potential. The helmeted honeyeater Lichenostomus melanops cassidix is a critically endangered subspecies of the common yellow-tufted honeyeater. Cassidix has declined to a single wild population of ~130 birds, despite being subject to intensive population management over recent decades. We assessed changes in microsatellite diversity in cassidix over the last four decades and used population viability analysis to explore whether genetic rescue through hybridization with the neighbouring Lichenostomus melanops gippslandicus subspecies constitutes a viable conservation strategy. The contemporary cassidix population is characterized by low genetic diversity and effective population size (N(e) < 50), suggesting it is vulnerable to inbreeding depression and will have limited capacity to evolve to changing environments. We find that gene flow from gippslandicus to cassidix has declined substantially relative to pre-1990 levels and argue that natural levels of gene flow between the two subspecies should be restored. Allowing gene flow (~4 migrants per generation) from gippslandicus into cassidix (i.e. genetic rescue), in combination with continued annual release of captive-bred cassidix (i.e. demographic rescue), should lead to positive demographic and genetic outcomes. Although we consider the risk of outbreeding depression to be low, we recommend that genetic rescue be managed within the context of the captive breeding programme, with monitoring of outcomes.

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Causes of hatching failure in endangered birds

Cited by 35 publications

References 30 publications

A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene

A Draft De Novo Genome Assembly for the Northern Bobwhite (Colinus virginianus) Reveals Evidence for a Rapid Decline in Effective Population Size Beginning in the Late Pleistocene

Role of propagule pressure in colonization success: disentangling the relative importance of demographic, genetic and habitat effects

Scope for genetic rescue of an endangered subspecies though re‐establishing natural gene flow with another subspecies

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