Landscape genetics is the scientific discipline that combines
population genetics
Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, ...
and
landscape ecology
Landscape ecology is the science of studying and improving relationships between ecological processes in the environment and particular ecosystems. This is done within a variety of landscape scales, development spatial patterns, and organizatio ...
. It broadly encompasses any study that analyses plant or animal population genetic
data
In the pursuit of knowledge, data (; ) is a collection of discrete Value_(semiotics), values that convey information, describing quantity, qualitative property, quality, fact, statistics, other basic units of meaning, or simply sequences of sy ...
in conjunction with data on the landscape features and
matrix
Matrix most commonly refers to:
* ''The Matrix'' (franchise), an American media franchise
** ''The Matrix'', a 1999 science-fiction action film
** "The Matrix", a fictional setting, a virtual reality environment, within ''The Matrix'' (franchis ...
quality where the sampled population lives. This allows for the analysis of
microevolutionary processes affecting the species in light of landscape spatial patterns, providing a more realistic view of how populations interact with their
environments.
Landscape genetics attempts to determine which landscape features are barriers to
dispersal and
gene flow, how human-induced landscape changes affect the
evolution
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
of populations, the
source-sink dynamics of a given population, and how
diseases or
invasive species spread across landscapes.
Landscape genetics differs from the fields of
biogeography and
phylogeography
Phylogeography is the study of the historical processes that may be responsible for the past to present geographic distributions of genealogical lineages. This is accomplished by considering the geographic distribution of individuals in light of ge ...
by providing information at finer temporal and spatial scales (i.e., at the level of individual genetic variation within a population). Because it focuses on sampling
individuals
An individual is that which exists as a distinct entity. Individuality (or self-hood) is the state or quality of being an individual; particularly (in the case of humans) of being a person unique from other people and possessing one's own need ...
, landscape genetics has the advantage of not having to subjectively define discrete populations prior to analysis.
Genetic tools are used to detect abrupt genetic differences between individuals within a population and
statistical tools are used to
correlate
In statistics, correlation or dependence is any statistical relationship, whether causal or not, between two random variables or bivariate data. Although in the broadest sense, "correlation" may indicate any type of association, in statistic ...
these genetic discontinuities with
landscape and environmental features.
The results of landscape genetics studies have potentially important applications to
conservation biology and
land management
Land management is the process of management, managing the land use, use and land development, development (in both Urban planning, urban and rural settings, but it is mostly managed in Urban places.) of Land (economics), land resources. Land reso ...
practices.
History
Landscape genetics emerged as its own
discipline after the seminal article entitled "Landscape genetics: combining landscape ecology and population genetics" by Manel et al. appeared in the journal ''Trends in Ecology and Evolution'' in 2003. According to that article, the concept that landscape patterns affect how organisms are distributed dates back to the 18th and 19th centuries in the writings of
Augustin Pyramus de Candolle
Augustin Pyramus (or Pyrame) de Candolle (, , ; 4 February 17789 September 1841) was a Swiss botanist. René Louiche Desfontaines launched de Candolle's botanical career by recommending him at a herbarium. Within a couple of years de Candoll ...
and
Alfred Russel Wallace.
The modern field is
interdisciplinary and integrates not only population genetics and landscape ecology, but also the field of
spatial statistics
Spatial analysis or spatial statistics includes any of the formal techniques which studies entities using their topological, geometric, or geographic properties. Spatial analysis includes a variety of techniques, many still in their early dev ...
.
As of 2008, over 655 articles had been published in the field in a variety of genetics and ecological
journals.
Advances and applications
Landscape genetics has advanced
ecological
Ecology () is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere level. Ecology overlaps wi ...
and
evolutionary
Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
theory
A theory is a rational type of abstract thinking about a phenomenon, or the results of such thinking. The process of contemplative and rational thinking is often associated with such processes as observational study or research. Theories may be ...
by facilitating an understanding of how gene flow and
adaptation occur in real
heterogeneous landscapes. It has also allowed for the estimation of functional connectivity across landscapes.
Elucidating landscape features that act as barriers or facilitators of
dispersal can inform the construction or preservation of
wildlife corridors that connect
fragmented landscapes. Landscape genetics can also help predict how diseases will spread across a landscape or how proposed management actions will affect populations. Finally, landscape genetics can help predict how well populations will adapt to continuing
global change
Global change in broad sense refers to planetary-scale changes in the Earth system. It is most commonly use to encompass the variety of changes connected to the rapid increase in human activities which started around mid-20th century, i.e. the ...
.
Methods
Genetic markers
Molecular markers A molecular marker is a molecule, sampled from some source, that gives information about its source. For example, DNA is a molecular marker that gives information about the organism from which it was taken. For another example, some proteins can be ...
of
genetic diversity such as DNA
microsatellites
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. ...
,
mitochondrial DNA,
amplified fragment length polymorphisms, and
alloenzymes are tested in random individuals of a particular species across a landscape.
These markers are used to determine the
genotype (genetic make-up) of the individuals tested.
Landscape and environmental features
Landscape features include
landscape composition (abundance and variety of
patch
Patch or Patches may refer to:
Arts, entertainment and media
* Patch Johnson, a fictional character from ''Days of Our Lives''
* Patch (''My Little Pony''), a toy
* "Patches" (Dickey Lee song), 1962
* "Patches" (Chairmen of the Board song) ...
types), landscape configuration (how these patches are arranged in space), and the quality of the
matrix
Matrix most commonly refers to:
* ''The Matrix'' (franchise), an American media franchise
** ''The Matrix'', a 1999 science-fiction action film
** "The Matrix", a fictional setting, a virtual reality environment, within ''The Matrix'' (franchis ...
(the space in a landscape between patches of habitat for a given species).
Topography
Topography is the study of the forms and features of land surfaces. The topography of an area may refer to the land forms and features themselves, or a description or depiction in maps.
Topography is a field of geoscience and planetary sc ...
,
altitude
Altitude or height (also sometimes known as depth) is a distance measurement, usually in the vertical or "up" direction, between a reference datum and a point or object. The exact definition and reference datum varies according to the context ...
,
habitat types, and potential barriers such as rivers or road are examples of landscape
variables.
Statistical tools
Identifying genetic patterns
Various statistical tools are utilized to identify genetic patterns from the genetic markers collected. Methods that
cluster
may refer to:
Science and technology Astronomy
* Cluster (spacecraft), constellation of four European Space Agency spacecraft
* Asteroid cluster, a small asteroid family
* Cluster II (spacecraft), a European Space Agency mission to study t ...
individuals into
subpopulations based on genetic differentiation or distance, such as
fixation index (FST) and
Bayesian assignment methods, are often used. However, because individuals are sometimes evenly distributed rather than spatially clustered across a landscape, these methods are limited and alternative methods are being developed.
Correlating genetic patterns to landscape
Statistical tools such as the
Mantel test or partial Mantel test are commonly used to
correlate
In statistics, correlation or dependence is any statistical relationship, whether causal or not, between two random variables or bivariate data. Although in the broadest sense, "correlation" may indicate any type of association, in statistic ...
genetic patterns with landscape features.
Linear regression models and
ordination
Ordination is the process by which individuals are consecrated, that is, set apart and elevated from the laity class to the clergy, who are thus then authorized (usually by the denominational hierarchy composed of other clergy) to perform v ...
techniques are also common.
Geographic information systems (GIS) can be used to visualize genetic patterns across space by plotting genetic data on a map of the landscape.
Example
A study published in 2012 analyzed the landscape genetics of
white tail deer
The white-tailed deer (''Odocoileus virginianus''), also known as the whitetail or Virginia deer, is a medium-sized deer native to North America, Central America, and South America as far south as Peru and Bolivia. It has also been introduced t ...
in
Wisconsin
Wisconsin () is a state in the upper Midwestern United States. Wisconsin is the 25th-largest state by total area and the 20th-most populous. It is bordered by Minnesota to the west, Iowa to the southwest, Illinois to the south, Lake M ...
and
Illinois
Illinois ( ) is a state in the Midwestern United States. Its largest metropolitan areas include the Chicago metropolitan area, and the Metro East section, of Greater St. Louis. Other smaller metropolitan areas include, Peoria and Rockf ...
. They
extracted DNA from the
lymph nodes
A lymph node, or lymph gland, is a kidney-shaped organ of the lymphatic system and the adaptive immune system. A large number of lymph nodes are linked throughout the body by the lymphatic vessels. They are major sites of lymphocytes that inclu ...
of 2,069
harvested deer across 64 townships. Fifteen microsatellite markers were used for
genotyping
Genotyping is the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence. ...
. A Bayesian population assignment test found no distinct subpopulations based on the genetic data.
Correlograms were used to elucidate fine-scale social structure, and found that more heavily
forested
A forest is an area of land dominated by trees. Hundreds of definitions of forest are used throughout the world, incorporating factors such as tree density, tree height, land use, legal standing, and ecological function. The United Nations' ...
and fragmented townships had more genetic relatedness between individual deer. Spatial
principal component analysis was used to elucidate broad-scale population connectivity. Partial Mantel tests found a correlation between genetic distance and geographic barriers, particularly roads and rivers. However, these were not absolute barriers and did not divide the deer into distinct subpopulations.
The finding of high genetic connectivity among the sampled deer has management implications for the setting of harvest number and population goals. The finding of high genetic connectivity also has implications for the spread of
chronic wasting disease
Chronic wasting disease (CWD), sometimes called zombie deer disease, is a transmissible spongiform encephalopathy (TSE) affecting deer. TSEs are a family of diseases thought to be caused by misfolded proteins called prions and include similar dis ...
among deer.
Sub-disciplines
Seascape genetics
Seascape genetics is a sub discipline of landscape genomics that scientists started to use in 2006.
The emergence of this field proceeded landscape genetics, advances in genetic laboratory technology, and higher resolution marine environmental data. Like landscape genetics, seascape genetics is a multidisciplinary field. Areas of expertise used in sea scape genetics includes oceanography, ecology, and population genetics.
Seascapes differ from landscapes due to differential connectivity in the aquatic environment. Currents allow for increased connectivity in some locations and restrict connectivity elsewhere. Many organisms that live in the ocean rely on currents to move their gametes and larvae which is called dispersal. Variable dispersal availability leads to subpopulations that have different structure; therefore, subpopulations are exposed to distinct selective pressures, experience separate rates of drift and have unique genetic diversity.
Seascape genomics is a tool that utilizes genetic markers in tandem with current patterns to better understand dispersal. Another key difference when studying marine systems is that many animals have extremely large population sizes. Substantial population sizes in the marine setting allows for greater adaptive potential with larger effective population size, meaning the portion of the population that is reproducing and passing along genes increases. A large population will have greater influence from selection than drift, thus marine organisms are more likely to have greater levels of local adaptation. In seascape analyses, genetic data allows for greater species understanding and tracking when the full life history is unknown or unable to be studied with ecology.
Population genetics incorporates many theories and techniques, all of which need to be taken into consideration for seascape and landscape analyses. There are several ways to collect genetic information. Popular methods in seascape genetics have been single nucleotide polymorphisms (SNPs), mitochondrial DNA, random amplified polymorphic DNAs, microsatellites, allozymes, and full genomes.
Collecting and processing sufficient samples has been a time-consuming process in the past. Next generation sequencing has helped to expand the field of landscape genomics because it allows for rapid sequencing of extremely large genomes.
Seascape genomics can be applied marine life with varying life histories to answer various questions about genetic influences on population dynamics. Analyzes on sessile organisms, animals such as clams that stay in the same place their whole life, can easily be analyzed to better understand environmental evolutionary pressures. One example, Salmoni et at used environmental data and genetic analysis to identify a heat tolerant gene in corals. Many other studies have been done on organisms such as oysters, seagrass, and mussels. Motile animals, animals that can move around, have also been studies through seascape genomics. DiBattista and his team studied how hydrodynamics influences snapper larval disbursement and were able to characterize connectivity between populations. Studies that utilize seascape genomics can be used in conservation and restoration efforts. This type of studies can help to define resilient individuals or classify areas that would be best for marine protected area due to their ecological purpose.
Landscape genomics
Landscape
genomics also correlates genetic data with landscape data, but the genetic data comes from multiple
loci (locations on a chromosome) across the genome of the organism, as in
population genomics Population genomics is the large-scale comparison of DNA sequences of populations. Population genomics is a neologism that is associated with population genetics. Population genomics studies genome-wide effects to improve our understanding of micro ...
. Landscape genetics typically measures less than a dozen different microsatellites in an organism, while landscape genomics often measures
single nucleotide polymorphisms at thousands of loci.
This allows for the identification of
outlier loci that may be under
selection
Selection may refer to:
Science
* Selection (biology), also called natural selection, selection in evolution
** Sex selection, in genetics
** Mate selection, in mating
** Sexual selection in humans, in human sexuality
** Human mating strateg ...
. Correlation to landscape data allows for identification of landscape factors contributing to genetic adaptation. This field is growing due to advances in
next-generation sequencing Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation ...
techniques.
Pitfalls
As a new and fast growing interdisciplinary field with no explicitly identified
best practices
A best practice is a method or technique that has been generally accepted as superior to other known alternatives because it often produces results that are superior to those achieved by other means or because it has become a standard way of doing ...
, it has been subject to a number of flaws in both study design and interpretation.
A 2016 publication
identified four common pitfalls of landscape genetics research that should be targeted for correction. These include assuming gene flow is always advantageous, over-generalizing results, failing to consider other processes that affect the
genetic structure
Genetic structure refers to any pattern in the genetic makeup of individuals within a population.
Genetic structure allows for information about an individual to be inferred from other members of the same population. In trivial terms, all popul ...
of populations, and mistaking
quantitative
Quantitative may refer to:
* Quantitative research, scientific investigation of quantitative properties
* Quantitative analysis (disambiguation)
* Quantitative verse, a metrical system in poetry
* Statistics, also known as quantitative analysis ...
methods for robust study design.
In particular, authors have been encouraged to report their
sampling design,
reproducibility of molecular data, and details on the
spatial data
Geographic data and information is defined in the ISO/TC 211 series of standards as data and information having an implicit or explicit association with a location relative to Earth (a geographic location or geographic position).
It is also cal ...
set and
spatial analyses utilized.
Because the effects of landscape on gene flow are not universal, sweeping generalities cannot be made, and species-specific studies are necessary.
Many of these pitfalls result from the interdisciplinary nature of landscape genetics, and could be avoided with better
collaboration among specialists in the fields of population genetics, landscape ecology, spatial statistics, and
geography
Geography (from Greek: , ''geographia''. Combination of Greek words ‘Geo’ (The Earth) and ‘Graphien’ (to describe), literally "earth description") is a field of science devoted to the study of the lands, features, inhabitants, an ...
.
References
{{Reflist
Population genetics
Landscape ecology