A Practical Guide for Genetic Management of Fragmented Animal and Plant Populations

2019 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Human Activity ◽  
Biological Diversity ◽  
Wild Animal ◽  
Isolated Populations ◽  
Genetic Management ◽  
Plant Populations ◽  
Practical Guide ◽  
Loss Of Genetic Diversity

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of wild animal and plant populations decreases and fragmentation increases, inbreeding reduces fitness and loss of genetic diversity reduces their ability to adapt to changes in the environment. Many small isolated populations are going extinct unnecessarily. In many cases, such populations can be genetically rescued by gene flow from another population within the species, but this is very rarely done. This book provides a practical guide to the genetic management of fragmented animal and plant populations.

Genetic Management of Fragmented Animal and Plant Populations

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Biological Diversity ◽  
Extinction Risk ◽  
Outbreeding Depression ◽  
Genetic Rescue ◽  
Isolated Populations ◽  
Genetic Management ◽  
Plant Populations ◽  
Loss Of Genetic Diversity

The biological diversity of the planet is being rapidly depleted due to the direct and indirect consequences of human activity. As the size of animal and plant populations decrease and fragmentation increases, loss of genetic diversity reduces their ability to adapt to changes in the environment, with inbreeding and reduced fitness inevitable consequences for many species. Many small isolated populations are going extinct unnecessarily. In many cases, such populations can be genetically rescued by gene flow into them from another population within the species, but this is very rarely done. This novel and authoritative book addresses the issues involved in genetic management of fragmented animal and plant populations, including inbreeding depression, loss of genetic diversity and elevated extinction risk in small isolated populations, augmentation of gene flow, genetic rescue, causes of outbreeding depression and predicting its occurrence, desirability and implementation of genetic translocations to cope with climate change, and defining and diagnosing species for conservation purposes.

Introduction

2019 ◽  
pp. 1-12
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Gene Flow ◽  
Global Climate Change ◽  
Global Climate ◽  
Extinction Risk ◽  
Genetic Erosion ◽  
Isolated Populations ◽  
Genetic Management ◽  
Loss Of Genetic Diversity

Genetic management of fragmented populations is one of the major, largely unaddressed issues in biodiversity conservation. Many species across the planet have fragmented distributions with small isolated populations that are potentially suffering from inbreeding and loss of genetic diversity (genetic erosion), leading to elevated extinction risk. Fortunately, genetic deterioration can usually be remedied by gene flow from another population (crossing between populations within species), yet this is rarely done, in part because of fears that crossing may be harmful (but we can predict when this will occur). We address management of gene flow between previously isolated populations and genetic management under global climate change.

Evolutionary genetics of small populations

2019 ◽  
pp. 15-30
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Population Size ◽  
Evolutionary Genetics ◽  
Small Population ◽  
Small Populations ◽  
Effective Population ◽  
Genetic Management ◽  
Loss Of Genetic Diversity ◽  
Number Of Individuals

Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift), and gene flow. Large outbreeding sexually reproducing populations typically contain substantial genetic diversity, while small populations typically contain reduced levels. Genetic impacts of small population size on inbreeding, loss of genetic diversity and population differentiation are determined by the genetically effective population size, which is usually much smaller than the number of individuals.

Introduction

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Climate Change ◽  
Gene Flow ◽  
Global Climate Change ◽  
Mating Systems ◽  
Global Climate ◽  
Extinction Risk ◽  
Genetic Erosion ◽  
Isolated Populations ◽  
Genetic Management ◽  
Loss Of Genetic Diversity

Genetic management of fragmented populations is one of the major, largely unaddressed issues in biodiversity conservation. Many species across the planet have fragmented distributions with small isolated populations that are potentially suffering from inbreeding and loss of genetic diversity (genetic erosion), leading to elevated extinction risk. Fortunately, genetic deterioration can usually be remedied by augmenting gene flow (crossing between populations within species), yet this is rarely done, in part because of fears that crossing may be harmful (but it is possible to predict when this will occur). Benefits and risks of genetic problems are sometimes altered in species with diverse mating systems and modes of inheritance. Adequate genetic management depends on appropriate delineation of species. We address management of gene flow between previously isolated populations and genetic management under global climate change.

scholarly journals Genetic monitoring of the greater stick-nest rat meta-population for strategic supplementation planning

2020 ◽  
Vol 21 (5) ◽  
pp. 941-956
Author(s):  
Lauren C. White ◽  
Vicki A. Thomson ◽  
Rebecca West ◽  
Laura Ruykys ◽  
Kym Ottewell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Species Conservation ◽  
Active Management ◽  
Isolated Populations ◽  
Single Nucleotide ◽  
Common Component ◽  
Loss Of Genetic Diversity ◽  
Source Populations ◽  
Effective Use

Abstract Translocation is an increasingly common component of species conservation efforts. However, translocated populations often suffer from loss of genetic diversity and increased inbreeding, and thus may require active management to establish gene flow across isolated populations. Assisted gene flow can be laborious and costly, so recipient and source populations should be carefully chosen to maximise genetic diversity outcomes. The greater stick-nest rat (GSNR, Leporillus conditor), a threatened Australian rodent, has been the focus of a translocation program since 1985, resulting in five extant translocated populations (St Peter Island, Reevesby Island, Arid Recovery, Salutation Island and Mt Gibson), all derived from a remnant wild population on the East and West Franklin Islands. We evaluated the genetic diversity in all extant GSNR populations using a large single nucleotide polymorphism dataset with the explicit purpose of informing future translocation planning. Our results show varying levels of genetic divergence, inbreeding and loss of genetic diversity in all translocated populations relative to the remnant source on the Franklin Islands. All translocated populations would benefit from supplementation to increase genetic diversity, but two—Salutation Island and Mt Gibson—are of highest priority. We recommend a targeted admixture approach, in which animals for supplementation are sourced from populations that have low relatedness to the recipient population. Subject to assessment of contemporary genetic diversity, St Peter Island and Arid Recovery are the most appropriate source populations for genetic supplementation. Our study demonstrates an effective use of genetic surveys for data-driven management of threatened species.

Evolutionary genetics of small populations

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Evolutionary Genetics ◽  
Small Population ◽  
Small Populations ◽  
Effective Population ◽  
Genetic Management ◽  
Evolutionary Genetic ◽  
Loss Of Genetic Diversity ◽  
Number Of Individuals

Genetic management of fragmented populations involves the application of evolutionary genetic theory and knowledge to alleviate problems due to inbreeding and loss of genetic diversity in small population fragments. Populations evolve through the effects of mutation, natural selection, chance (genetic drift) and gene flow (migration). Large outbreeding, sexually reproducing populations typically contain substantial genetic diversity, while small populations typically contain reduced levels. Genetic impacts of small population size on inbreeding, loss of genetic diversity and population differentiation are determined by the genetically effective population size, which is usually much smaller than the number of individuals.

Genetic Differentiation in Isolated Populations of Hakea carinata (Proteaceae)

1998 ◽  
Vol 46 (6) ◽  
pp. 671 ◽  
Author(s):  
G. J. Starr ◽  
S. M. Carthew
Keyword(s):  
Gene Flow ◽  
Habitat Fragmentation ◽  
Gene Diversity ◽  
South Australia ◽  
Similar Species ◽  
Isolated Populations ◽  
Plant Populations ◽  
Evolutionary Condition ◽  
Private Alleles

Fragmentation of the landscape by human activity has created small, isolated plant populations. Hakea carinata F. Muell. ex Meissner, a sclerophyllous shrub, is common in isolated fragments of vegetation in South Australia. This study investigated whether habitat fragmentation has caused restrictions to gene flow between populations. Gene diversity (HT = 0.317) is average for similar species but little is held within populations (HS = 0.168) and 46.9% of gene diversity is accounted for between populations. Estimates of gene flow are NM = 0.270 (based on FST) and NM = 0.129 (based on private alleles). Populations are substantially selfing (t = 0.111). Small isolated populations appears to be a long-term evolutionary condition in this species rather than a consequence of habitat fragmentation; however, population extinctions are occurring. Conservation will require the reservation of many populations to represent the genetic variation present in the species.

Inbreeding and loss of genetic diversity increase extinction risk

2019 ◽  
pp. 31-48
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Inbreeding Depression ◽  
Environmental Changes ◽  
Extinction Risk ◽  
Raw Material ◽  
Heterozygote Advantage ◽  
Isolated Populations ◽  
Survival And Reproduction ◽  
Loss Of Genetic Diversity ◽  
Harmful Effects

Inbreeding reduces survival and reproduction (i.e. it causes inbreeding depression), and thereby increases extinction risk. Inbreeding depression is due to increased homozygosity for harmful alleles and at loci exhibiting heterozygote advantage. Inbreeding depression is nearly universal in sexually reproducing organisms that are diploid or have higher ploidies. Impacts of inbreeding are generally greater in species that naturally outbreed than those that inbreed, in stressful than benign environments, and for fitness than peripheral traits. Harmful effects accumulate across the life cycle, resulting in devastating effects on total fitness in outbreeding species.Species face ubiquitous environmental change and must adapt or they will go extinct. Genetic diversity is the raw material required for evolutionary adaptation. However, loss of genetic diversity is unavoidable in small isolated populations, diminishing their capacity to evolve in response to environmental changes, and thereby increasing extinction risk.

scholarly journals Evaluation of the Romosinuano cattle population structure in Mexico using pedigree analysis

2020 ◽  
Vol 33 (1) ◽  
pp. 44-59
Author(s):  
Rafael Núñez-Domínguez ◽  
Ricardo E Martínez-Rocha ◽  
Jorge A Hidalgo-Moreno ◽  
Rodolfo Ramírez-Valverde ◽  
José G García-Muñiz
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Pedigree Analysis ◽  
Effective Population ◽  
Genetic Management ◽  
Generation Interval

Background: Romosinuano cattle breed in Mexico has endured isolation and it is necessary to characterize it in order to facilitate sustainable genetic management. Objective: To assess the evolution of the structure and genetic diversity of the Romosinuano breed in Mexico, through pedigree analysis. Methods: Pedigree data was obtained from Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). The ENDOG program (4.8 version) was used to analyze two datasets, one that includes upgrading from F1 animals (UP) and the other with only straight-bred cattle (SP). For both datasets, three reference populations were defined: 1998-2003 (RP1), 2004-2009 (RP2), and 2010-2017 (RP3). The pedigree included 3,432 animals in UP and 1,518 in SP. Demographic parameters were: Generation interval (GI), equivalent number of generations (EG), pedigree completeness index (PCI), and gene flow among herds. Genetic parameters were: Inbreeding (F) and average relatedness (AR) coefficients, effective population size (Nec), effective number of founders and ancestors, and number of founder genome equivalents. Results: The GI varied from 6.10 to 6.54 for UP, and from 6.47 to 7.16 yr for SP. The EG of the UP and SP improved >63% from RP1 to RP3. The PCI increased over time. No nucleus or isolated herds were found. For RP3, F and AR reached 2.08 and 5.12% in the UP, and 2.55 and 5.94% in the SP. For RP3, Nec was 57 in the UP and 45 in the SP. Genetic diversity losses were attributed mainly (>66%) to genetic drift, except for RP3 in the SP (44%). Conclusions: A reduction of the genetic diversity has been occurring after the Romosinuano breed association was established in Mexico, and this is mainly due to random loss of genes.Keywords: effective population size; gene flow; genetic diversity; genetic drift; generation interval; inbreeding; pedigree; population structure; probability of gene origin; Romosinuano cattle. Resumen Antecedentes: La raza bovina Romosinuano ha estado prácticamente aislada en México y requiere ser caracterizada para un manejo genético sostenible. Objetivo: Evaluar la evolución de la estructura y diversidad genética de la raza Romosinuano en México, mediante el análisis del pedigrí. Métodos: Los datos genealógicos provinieron de la Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). Los análisis se realizaron con el programa ENDOG (versión 4.8) para dos bases de datos, una que incluyó animales en cruzamiento absorbente (UP) a partir de F1 y la otra con sólo animales puros (SP). Para ambas bases de datos se definieron tres poblaciones de referencia: 1998-2003 (RP1), 2004- 2009 (RP2), y 2010-2017 (RP3). El pedigrí incluyó 3.432 animales en la UP y 1.518 en la SP. Los parámetros demográficos fueron: intervalo generacional (GI), número de generaciones equivalentes (EG), índice de completitud del pedigrí (PCI), y flujo de genes entre hatos. Los parámetros genéticos fueron: coeficientes de consanguinidad (F) y de relación genética aditiva (AR), tamaño efectivo de la población (Nec), número efectivo de fundadores y ancestros, y número equivalente de genomas fundadores. Resultados: El GI varió de 6,10 a 6,54 para la UP, y de 6,47 a 7,16 años para la SP. El EG de la UP y la SP mejoró >63%, de RP1 a RP3. El PCI aumentó a través de los años, pero más para la SP que para la UP. No se encontraron hatos núcleo o aislados. Para RP3, F y AR alcanzaron 2,08 y 5,12% en la UP, y 2,55 y 5,94% en la SP. Para RP3, Nec fue 57 en la UP y 45 en la SP. Más de 66% de las pérdidas en diversidad genética se debieron a deriva genética, excepto para RP3 en la UP (44%). Conclusiones: una reducción de la diversidad genética ha estado ocurriendo después de que se formó la asociación de criadores de ganado Romosinuano en México, y es debida principalmente a pérdidas aleatorias de genes.Palabras clave: consanguinidad; deriva genética; diversidad genética; estructura poblacional; flujo de genes; ganado Romosinuano; intervalo generacional; pedigrí; probabilidad de origen del gen; tamaño efectivo de población. Resumo Antecedentes: A raça bovina Romosinuano tem estado praticamente isolada no México e precisa ser caracterizada para um manejo genético sustentável. Objetivo: Avaliar a evolução da estrutura e diversidade genética da raça Romosinuano no México, através da análise de pedigree. Métodos: Os dados genealógicos vieram da Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). As análises foram feitas com o programa ENDOG (versão 4.8) para duas bases de dados, uma que incluiu animais em cruzamento absorvente (UP) a partir da F1 e a outra base de dados somente com animais puros (SP). Para ambas bases de dados foram definidas três populações de referência: 1998-2003 (RP1), 2004-2009 (RP2) e 2010-2017 (RP3). O pedigree incluiu 3.432 animais na UP e 1.518 na SP. Os parâmetros demográficos foram: intervalo entre gerações (GI), número de gerações equivalentes (EG), índice de completude do pedigree (PCI), e fluxo de genes entre rebanhos. Os parâmetros genéticos foram: coeficiente de consanguinidade (F) e da relação genética aditiva (AR), tamanho efetivo da população (Nec), número efetivo de fundadores e ancestrais, e número equivalente de genomas fundadores. Resultados: O GI variou de 6,10 a 6,54 para a UP, e de 6,47 a 7,16 anos para a SP. EG da UP e a SP melhorou >63%, de RP1 a RP3. O PCI aumentou ao longo dos anos, mas mais para a SP do que para o UP. Não se encontraram rebanhos núcleo ou isolados. Para RP3, F e AR alcançaram 2,08 e 5,12% na UP, e 2,55 e 5,94% na SP. Para RP3, Nec foi 57 na UP e 45 na SP. Mais de 66% das perdas em diversidade genética foram ocasionadas pela deriva genética, exceto para RP3 no UP (44%). Conclusões: Depois que a associação da raça Romosinuano foi estabelecida no México, tem ocorrido uma redução da diversidade genética, principalmente devido a perdas aleatórias de genes.Palavras-chave: consanguinidade; deriva genética; diversidade genética, estrutura populacional; fluxo de genes; intervalo entre gerações; pedigree; probabilidade de origem do gene; Romosinuano; tamanho efetivo da população.

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