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Bee conservation in the age of genomics

June 2017
Conservation Genetics 18(3)

June 2017
18(3)

Authors:

York University

Many wild and managed bee pollinators have experienced population declines over the past several decades, and molecular and population genetic tools have been valuable in understanding conservation threats across the bee tree of life. Emerging genomic tools have the potential to improve classical applications of conservation genetics, such as assessing species status, and quantifying genetic diversity, gene flow and effective population sizes. Genomic tools can also revolutionize novel research in bee conservation and management, including the identification of loci underlying adaptive and economically desirable traits, such as those involved in disease susceptibility, responses to multiple environmental stressors, and even discovering and understanding the hidden diversity of beneficial microorganisms associated with bees. In this perspective, we provide a survey of some of the ways genomic tools can be applied to bee conservation to bridge the gap between basic and applied genomics research.

Overview of genomic tools and applications for bee conservation. a Broad sense conservation genomics utilizes HTS and reduced genome high through put sequencing (rHTS) to genotype thousands of SNPs to enhance resolution for classic questions in conservation genetics, such as the size and connectivity of populations targeted for conservation, resolving demographic history, and to define evolutionary distinct lineages that require special management attention. b Narrow sense conservation genomics utilize ‘omic tools to go beyond the traditional conservation genetics paradigm to develop tools for species conservation and management. HTS greatly facilities research that links mutations with specific traits and fitness in natural and managed populations, and allows bee conservation biologists to directly identify loci that are important for fitness (e.g. resistance to diseases, agrochemical, and the ability for populations to adapt to climate change), and potentially implement genomic-assisted breeding programs for recovery or management. Metagenomics provides a very rapid way to identify organisms that are detrimental (i.e. parasites and pathogens) or beneficial (i.e. gut microbiota) to bees. Similar to human medicine, gene expression profiling using RNAseq can be used to develop diagnostic markers for bee health, which can be used in a monitoring and compliance setting

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RESEARCH ARTICLE

Bee conservation in the age of genomics

Jeffrey D. Lozier

•Amro Zayed

Received: 14 April 2016 / Accepted: 4 October 2016

ÓSpringer Science+Business Media Dordrecht 2016

Abstract Many wild and managed bee pollinators have

experienced population declines over the past several

decades, and molecular and population genetic tools have

been valuable in understanding conservation threats across

the bee tree of life. Emerging genomic tools have the

potential to improve classical applications of conservation

genetics, such as assessing species status, and quantifying

genetic diversity, gene ﬂow and effective population sizes.

Genomic tools can also revolutionize novel research in bee

conservation and management, including the identiﬁcation

of loci underlying adaptive and economically desirable

traits, such as those involved in disease susceptibility,

responses to multiple environmental stressors, and even

discovering and understanding the hidden diversity of

beneﬁcial microorganisms associated with bees. In this

perspective, we provide a survey of some of the ways

genomic tools can be applied to bee conservation to bridge

the gap between basic and applied genomics research.

Keywords Bees Pollination Population genetics 

Transcriptomics Genome wide association mapping 

Ecological genomics

Introduction

The world’s more than 16,000 bee species are critical

components of both natural and human-modiﬁed terrestrial

ecosystems (Michener 2000; Danforth 2007). Over the past

several decades, evidence has accumulated for the often

rapid decline of many managed and wild pollinator species

throughout the globe (Brown and Paxton 2009; Williams

and Osborne 2009; Neumann and Carreck 2010; Potts et al.

2010; Cameron et al. 2011). At the same time, many spe-

cies remain common and successful in their native ranges,

raising questions as to how species-speciﬁc genetic and life

history traits inﬂuence susceptibility and resistance to

factors impacting population health. Given the expected

ecological and economic ramiﬁcations of pollinator decli-

nes for both managed and native species (Kremen et al.

2002; Biesmeijer et al. 2006; Garibaldi et al. 2013), bees

have emerged as a ﬂagship group for revealing the ways in

which anthropogenic modiﬁcation of landscapes is

impacting biodiversity, attracting signiﬁcant attention from

scientists, the public, and policy-makers.

Genetics has played a key role in conservation biology as

molecular tools have enabled studies of key conservation

parameters that were previously very difﬁcult—if not

impossible—to estimate; including species identity, popu-

lation structure, levels of gene ﬂow, genetic diversity,

inbreeding and relatedness, and occurrence of past events

such as population bottlenecks, expansions, or changes in

connectivity (Allendorf et al. 2013). The increasing avail-

ability of genomic tools, accelerated through novel appli-

cations and decreasing costs of massively parallel high-

throughput sequencing (HTS) technologies and computa-

tional resources, will create new avenues for research in the

ﬁeld of conservation genetics (Avise 2009; Ouborg et al.

2010; Allendorf et al. 2010). In addition to increasing the

&Jeffrey D. Lozier

jlozier@ua.edu

Amro Zayed

zayed@yorku.ca

Department of Biological Sciences, University of Alabama,

Tuscaloosa, AL 35487, USA

Department of Biology, York University, 4700 Keele Street,

Toronto, ON M3J 1P3, Canada

123

Conserv Genet

DOI 10.1007/s10592-016-0893-7

resolution and power of traditional population genetics

applications (so-called ‘‘broad sense’’ conservation geno-

mics sensu Garner et al. 2016), genomics approaches are

beginning to allow researchers to test new, or previously

intractable, hypotheses about the functional signiﬁcance of

genetic variation and the genetic architecture underlying

many ecological and evolutionary important traits and pro-

cesses (‘‘narrow sense’’ conservation genomics). Moreover,

genomic tools can be directly used in wildlife management

by helping to diagnose the causes of population declines, for

testing the health of managed wildlife populations, and by

directly improving the ﬁtness of managed populations

through ‘omics assisted breeding.

Molecular and population genetics have greatly enhanced

our understanding of pollinator conservation biology (re-

viewed in Packer and Owen 2001;Zayed2009; Woodard et al.

2015). Population genetics research conducted over the past

several decades has helped elucidate general patterns of

population structure and gene ﬂow, mating systems, and

effective population sizes of both common and declining

pollinator species. In this perspective, we highlight some of

the recent, ongoing, and future advances that the ﬁeld of

genomics for bee biology and conservation. We brieﬂy review

some of the genetic considerations that may be relevant for bee

conservation and provide an overview of currently developed

conservation genomics tools. We then review some of the

improvements genomic techniques can make on traditional

conservation genetics inquires (e.g. population structure, gene

ﬂow; Fig. 1a), followed by a discussion of novel contributions

that will stem from the application of genomics to diagnose,

monitor and manage the health of bee populations (Fig. 1b).

Finally, we provide some practical issues regarding

sequencing strategies, sampling and data analysis that should

be considered as bee researchers transition from PCR-based

population genetics toward genomic approaches.

Genetic considerations for bee conservation

A central concept of conservation genetics is that small,

isolated populations have an increased risk of extinction

from intrinsic factors including genetic drift and inbreeding

(Amos and Balmford 2001; Frankham 2005; Laikre et al.

2010), and that molecular tools combined with population

genetics theory can reveal the signatures of such threats.

Bees are certainly at risk from commonly invoked threats,

such as land use changes and habitat fragmentation, the

potential effects of which are starkly illustrated by com-

paring population genetics of mainland and island popu-

lations (Lozier et al. 2011; Boff et al. 2014; Jha 2015).

However, bees may be especially susceptible to changes in

their habitat size and connectivity because of several

intrinsic, and often unique, life history characteristics.

Bees are haplodiploid (diploid females and haploid

males) and are expected to have approximately 75 % of the

genetic diversity expected for an equivalent number of

diploid individuals on average (Packer and Owen 2001).

Associated with this haplodiploidy, complementary sex

determination can lead to the production of sterile diploid

males when population sizes are small, or in large popula-

tions with mating systems that incorporate inbreeding,

which can place an additional genetic burden on populations

(Zayed and Packer 2005; Zayed 2009; Harpur et al. 2013b).

Complex life histories may also make bees more susceptible

to habitat loss and other extrinsic environmental changes.

For example, many bees require diverse sets of resources

throughout their lifecycle (e.g., suitable sites for hibernation

and nesting, foraging resources available throughout the

colony cycle) that can be affected by urbanization, agri-

cultural intensiﬁcation, climate change, and deforestation.

In some species, this could be exacerbated by a high degree

of nest-site philopatry (Lo

´pez-Uribe et al. 2015), resource

specialization (i.e. oligolectic vs polylectic bees) (Danforth

et al. 2003; Packer et al. 2005; Cane et al. 2006; Zayed et al.

2006; Zayed and Packer 2007) or mating strategies (e.g.,

monandry vs. polyandry; systematic inbreeding vs.

inbreeding avoidance) (Paxton 2005). The degree of

sociality may inﬂuence population genetic processes that

can alter genetic variation, including discrepancies between

numbers of reproductive vs sterile individuals, aggregation

of related individuals, or variance in reproduction between

colonies (Pamilo et al. 1997; Chapman and Bourke 2001;

Ulrich et al. 2009). Bee species that are intensively managed

may suffer from other genetic threats. Managed species are

commonly reared or transported under conditions that

facilitate disease transmission, and both managed bumble-

bees and honey bees have a list of serious pests and

pathogens that can ‘spillover’ into natural populations

(Colla et al. 2006; Meeus et al. 2011; Graystock et al. 2013;

Cameron et al. 2016). Domestication bottlenecks are often

associated with declines in genetic diversity in livestock,

and this may be true for managed bumblebees. However,

migratory beekeeping practices along with the mating

biology of honey bees have led to managed honey bee

populations that have high levels of genetic diversity

(Harpur et al. 2012,2013a), although these admixed geno-

types may threaten the genetic integrity of native and locally

adapted Apis mellifera populations (De La Ru

´a et al. 2013).

Finally, recent genome sequencing efforts suggest that

bees, including honey bees, bumble bees, and leafcutting

bees, may be depauperate in xenobiotic detoxiﬁcation and

immune genes compared to other insects (Weinstock et al.

2006; Barribeau et al. 2015; Sadd et al. 2015). Comparative

genomics provides support for a reduced classical immune

repertoire prior to the evolution of complex sociality,

perhaps stemming back to the common ancestor of bees

Conserv Genet

123

(Barribeau et al. 2015). In the honey bee, evidence for

relaxed selective constraints among innate immunity genes

over the past 5 to 25 million years (Harpur and Zayed

2013) may reﬂect simpliﬁcation of the honey bee innate

immune system over evolutionary timescales. Reductions

in innate immune and detoxiﬁcation genes may increase

susceptibility to parasites and agrochemicals, which are

hypothesized to play a major role in the declines of many

managed and native bees (Cox-Foster et al. 2007; Cameron

et al. 2011; Meeus et al. 2011; Furst et al. 2014). Pollina-

tors in agro-environments encounter a long list of agro-

chemicals (Mullin et al. 2010), some of which, like

neonicotinoid insecticides, are highly toxic to bees.

Reductions of their detoxiﬁcation systems may thus make

bees highly susceptible to combinations of agrochemicals

that often act synergistically (Johnson et al. 2013).

Importantly, however, these patterns may not be biologi-

cally signiﬁcant if bees make use of non-canonical immune

genes to combat infections (Grozinger and Robinson

2015).

Genomic tools for conservation genetics

High-throughput sequencing approaches are rapidly revo-

lutionizing the ﬁeld of population and conservation genetics

(Andrews and Luikart 2014). Much of the research in con-

servation genetics focuses on population genetics issues such

as assessing heterozygosity, gene ﬂow and taxonomy. HTS

can be ﬂexibly applied to such studies (Fig. 1a), depending

on the goal or required resolution, ranging from de novo

sequencing of novel genomes in a small number of samples,

(a) Broad Sense Conservation Genomics

HTS & rHTS

SNPs

Conservation

Parameters

Gene Flow

Population Size

Inbreeding & Relatedness

Demography

History

Bottlenecks

Introgression

Ancestry

Taxonomy

Cryptic Species

Evolutionarily Significant

Units

Invasive Species

(b) Narrow Sense Conservation Genomics

Genomic HTS

SNPs

Genotype to

Phenotype

GWAS

Population Contrasts

Genotype to

Fitness

Natural Selection

Local Adaptaion

Extra-

Organisms

Pathogens

Parasites

Gut fauna

Biomarkers

for

Bee Health

Meta ‘omics

RNAseq

Expression

tool

data

application tooldataapplication

Fig. 1 Overview of genomic tools and applications for bee conser-

vation. aBroad sense conservation genomics utilizes HTS and

reduced genome high through put sequencing (rHTS) to genotype

thousands of SNPs to enhance resolution for classic questions in

conservation genetics, such as the size and connectivity of popula-

tions targeted for conservation, resolving demographic history, and to

deﬁne evolutionary distinct lineages that require special management

attention. bNarrow sense conservation genomics utilize ‘omic tools

to go beyond the traditional conservation genetics paradigm to

develop tools for species conservation and management. HTS greatly

facilities research that links mutations with speciﬁc traits and ﬁtness

in natural and managed populations, and allows bee conservation

biologists to directly identify loci that are important for ﬁtness (e.g.

resistance to diseases, agrochemical, and the ability for populations to

adapt to climate change), and potentially implement genomic-assisted

breeding programs for recovery or management. Metagenomics

provides a very rapid way to identify organisms that are detrimental

(i.e. parasites and pathogens) or beneﬁcial (i.e. gut microbiota) to

bees. Similar to human medicine, gene expression proﬁling using

RNAseq can be used to develop diagnostic markers for bee health,

which can be used in a monitoring and compliance setting

Conserv Genet

123

re-sequencing of entire genomes from individuals or pools of

individuals, to targeted sequencing of genomic subsamples

in moderate to large numbers of individuals. These genomic

tools will also be valuable for addressing more mechanistic

questions (Fig. 1b), including assaying selection signatures

and global gene expression to identify responses to envi-

ronmental stressors.

Increasing availability of genomic resources for bees

Genome sequences are currently available for at least 11 bee

species (Weinstock et al. 2006; Kocher et al. 2013; Kapheim

et al. 2015; Park et al. 2015; Sadd et al. 2015). These include

several honey bee species (Apis mellifera,A. dorsata,A.

cerana), two bumble bee species (Bombus impatiens and B.

terrestris), the stingless bee Melipona quadrifasciata, two

long-tongued bees including the leaf-cutting bee Megachile

rotundata and Habropoda laboriosa, two short-tongued

sweat bees Dufourea novaeangliae and Lasioglossum

albipes, and the orchid bee Eufriesea mexicana. Up-to-date

information on bee genomes and genomic resources can be

found at NCBI’s genome database for the Apoidea (http://

www.ncbi.nlm.nih.gov/genome/?term=apoidea), and Bee-

Base (http://hymenopteragenome.org/beebase/). Bee gen-

omes sequenced to date are all from common species (i.e.

not of conservation concern), several of which are actively

managed for pollination, and many belong to the corbiculate

bees, such as honey bees and bumble bees, which are

agriculturally important and also serve as model organisms

for the study of animal behavior. Despite the taxonomic and

ecological biases, the available genomes are an immense

community resource and provide a springboard for studies

in bee species of conservation concern. For example, the

available bee genomes can be used for designing PCR pri-

mers for candidate gene sequencing and gene expression

analysis (e.g., quantitative PCR), in addition to anchoring

the assembly of genomic data from closely related species

and providing information for annotating new bee genomes.

Sequencing new bee genomes is likely to be facilitated by

sequencing haploid males, which greatly aids assembly and

detection of errors compared to diploid genomes.

Whole genome resequencing

Studies that re-sequence genomes (or portions of genomes,

see below) from multiple individuals per species (i.e. true

population genomics) will become increasingly feasible as

the number of available bee genomes grows, and the cost

of sequencing declines. To date, whole genome population

genetics has been restricted to honey bees (Harpur et al.

2014; Wallberg et al. 2014; Wragg et al. 2016). Re-se-

quencing of many populations and individuals at a spatial

resolution typical of more traditional molecular studies (i.e.

hundreds of individuals) will remain cost-prohibitive for

most bee species, although sequencing haploid males is

cost effective because they can be sequenced at lower

coverage relative to the diploid females (Wragg et al.

2016). HTS of pools of individuals (PoolSeq) may offer a

reasonable compromise (Fabian et al. 2012; Schlo

¨tterer

et al. 2014; Hasselmann et al. 2015). In PoolSeq, DNA

isolates from multiple individuals per population are

pooled into a single DNA sample and each pooled popu-

lation library, rather than each individual, receives a unique

molecular barcode for sequencing. PoolSeq appears to

provide accurate allele frequency and parameter estimates

compared to individual sequencing but relies on large

population samples, and thus may not be suitable for rare

or declining species (Schlo

¨tterer et al. 2014). In eusocial

bees, the risk of sampling multiple individuals per colony

will offer another potential challenge for PoolSeq; in many

traditional population genetic analyses of bees, siblings are

often identiﬁed and excluded from analyses post hoc to

avoid biasing allele frequency estimates by grouping sets

of close relatives (e.g., Lozier et al. 2011), but this would

be challenging or impossible in pooled samples. The effect

of pooling families within populations will likely depend

on the exact makeup of the sample, and the impact of

sociality on parameter inference via PoolSeq would be

worth investigating with simulation studies.

Transcriptomics, genome reduction, and target

capture methods

RNA sequencing

RNA sequencing (RNAseq) has revolutionized studies of

gene expression through direct analysis of global transcript

abundance (Marioni et al. 2008). RNAseq is powerful for

non-model organisms because it does not require a

sequenced genome and associated gene predictions;

indeed, it is common to construct a de novo transcriptome

assembly from RNAseq data (Vijay et al. 2013). As bee

genomes accumulate, alignment of RNAseq data to a clo-

sely related transcriptome may be increasingly feasible,

however, as recently illustrated by successful mapping of

RNAseq data from the bumble bee Bombus bifarius to the

B. impatiens genome (Lozier et al. 2016). Many of the

greatest impacts for RNAseq data in bees are likely to

come from quantifying how gene regulation responds to

environmental pressures such as thermal regimes (Torson

et al. 2015), pathogens (Cornman et al. 2013b; Galbraith

et al. 2015), pesticides (Aufauvre et al. 2014), or diet (Mao

et al. 2013; Wheeler and Robinson 2014); here, RNAseq

approaches are expected to be superior to probe-based

microarrays because they allow the discovery of taxon-

speciﬁc genes associated with response to stress and may

Conserv Genet

123

be less limited by existing genomic resources for the target

species. In addition to gene expression data, RNAseq

simultaneously provides raw sequence data for calling

single nucleotide polymorphisms (SNPs) from expressed

regions of the genome that can be used for population

genetics (Renaut et al. 2010; De Wit et al. 2015; Lozier

et al. 2016). A number of challenges including cost,

specimen handling and RNA isolation, and variant calling

may make other HTS strategies more useful for genotyping

large samples, but population genetic analysis of high

expression genes from RNAseq data maybe very useful in

some contexts. Transcriptome data have been generated

from diverse bees, including Apidae (honey bees, bumble

bees, orchid bees, stingless bees, carpenter bees),

Megachilidae, and Halictidae (e.g., Woodard et al. 2011;

Rehan et al. 2015; Jones et al. 2015; Lozier et al. 2016).

Reduced complexity high throughput sequencing (rHTS)

Several approaches have become available to reduce genomic

complexity for DNA-based HTS. The most prevalent method

is restriction site associated DNA sequencing (RADseq),

which relies on restriction enzyme fragmentation of the gen-

ome, and sequencing of individually barcoded libraries (re-

viewed in Davey and Blaxter 2010; Andrews et al. 2016).

There are several variations to RADseq available, as well as

other genotyping-by-sequencing approaches, that may work

well for particular samples or study designs, and require less

technical expertise. The diversity of approaches, and possible

strengths and weaknesses for different applications, have been

reviewed elsewhere (e.g., (Davey et al. 2011; Peterson et al.

2012;Arnoldetal.2013; Davey et al. 2013;Puritzetal.2014;

Andrews et al. 2014,2016). The value of RADseq is that

genome-wide variant data for population genomics and

mapping quantitative trait loci (QTL) underlying conserva-

tion-relevant traits (Hohenlohe et al. 2010; Weber et al. 2013)

can be generated in species where whole genome wide asso-

ciation mapping approaches are not feasible. Loci can be

obtained at a desired density if something is known about

restriction site frequencies for different enzymes, and geno-

typing can be conducted by mapping either to an existing

genome or using de novo assembly approaches (Catchen et al.

2013). In bumble bees, both approaches appear to provide

similar estimates for diversity parameters (Lozier 2014;Sadd

et al. 2015), although positioning data from genome mapping,

when available, will provide opportunities for more sophisti-

cated analyses.

Target capture

Several methods make use of sequence capture hybridiza-

tion techniques to target HTS toward particular regions of

the genome (e.g., exon-capture, ultra-conserved element,

RAD loci) (Yi et al. 2010; Faircloth et al. 2012; Suchan

et al. 2016). These approaches may be particularly valuable

as they allow sequencing effort to focus on speciﬁc regions

of interest (e.g., coding vs. noncoding regions) and may

perform well with degraded DNA (McCormack et al.

2015). As genomes accumulate across the bee phylogeny,

it will be increasing feasible to design conserved target

capture probe sets for genomic regions and species of

interest. A set of general Hymenopteran ultraconserved

elements has been developed (Faircloth et al. 2015), and

may provide a useful HTS resource for some applications.

Broad-sense conservation genomics strategies

for bees

Genetic diversity in wild and managed bee

populations

Genetic diversity and population size are considered key

parameters of interest in many conservation genetics

applications (Laikre et al. 2010). Small population sizes

exacerbate loss of alleles from genetic drift and inbreeding

among close relatives, resulting in increasing homozygosity

that can reduce individual ﬁtness and decrease population

viability or adaptive potential, and increase susceptibility to

stochastic demographic effects (Frankham 1996). In social

bees, for example, genetic diversity at the population or

colony level may be associated with conservation threats

such as susceptibility to parasites (Mattila and Seeley 2007;

Whitehorn et al. 2009,2011). Populations are expected to

lose genetic diversity at a rate inversely proportional to

effective population size, so small populations should have

reduced levels of genetic diversity (e.g. heterozygosity at

marker loci or nucleotide diversity of DNA sequences)

compared to larger populations. Estimates of genetic

diversity may thus provide additional information on pop-

ulation health from both demographic and genetic per-

spectives. Comparisons of heterozygosity differences

among bee species have thus commonly been reported as a

tool to identify conservation concerns (Zayed et al. 2006;

Goulson et al. 2008; Cameron et al. 2011; Maebe et al.

2015), with a general trend suggesting reduced diversity in

more threatened species.

One issue with drawing conclusions from comparisons

of diversity is that both effective population size and

mutation rate inﬂuence heterozygosity of neutral loci at

mutation-drift equilibrium (Charlesworth 2009). Thus,

although small populations are expected to harbor reduced

levels of genetic diversity compared to large populations,

low mutation rates may have the same effect. Mutation

rates of commonly used markers, such as microsatellites,

will vary from locus to locus (Ellegren 2004), meaning that

Conserv Genet

123

valid comparisons of diversity among intra- or interspeciﬁc

populations should utilize the same sets of loci and must

avoid systematic missing data. The large numbers of

microsatellites that have been discovered to amplify across

species within bee genera have aided such comparisons

(e.g., for bumble bees: Reber Funk et al. 2006; Stolle et al.

2009; Lozier et al. 2011; for sweat bees: Zayed 2006).

Perhaps more problematic, however, is that even when the

same microsatellite loci are compared across species,

mutation rates vary among taxa (Ellegren 2000; Webster

et al. 2002), further complicating interspeciﬁc comparisons

of genetic diversity. NGS resources have the potential to

overcome many of these limitations. Although individual

nucleotides provide limited information on genetic diver-

sity, across large regions of genome sequence, patterns of

mutation are more straightforward to model and should be

more comparable, at least among closely related species.

Nonetheless, HTS-based approaches offer their own sets of

biases in diversity estimation, including heterozygote drop-

out in low coverage datasets or loss of restriction cut sites

through mutation in genome reduction approaches such as

RADseq (Nielsen et al. 2012; Arnold et al. 2013). Methods

exist for correcting some of these biases (Korneliussen

et al. 2013). Finally, it must also be recognized that highly

variable multi-allelic and DNA sequence based markers

may reveal the signatures of processes at different time-

scales, and in many conservation genetics studies where

recent demographic changes are layered onto more ancient

phylogeographic structure, it may be valuable to compare

and contrast signals across different marker types. The

potential complexities associated with genetic diversity

estimates across species using different classes of tradi-

tional and HTS-based markers (RADseq) was recently

illustrated for two bumble bee species that have experi-

enced differing recent demographic trajectories (Lozier

2014).

Improving estimates of individual relatedness

Although social bee species represent a minority of the

total bee diversity (Michener 2000), a substantial fraction

of conservation genetics research in bees has dealt with

estimating kinship among individuals. Worker bees from

the same colony for many bumble bee species, for exam-

ple, will be full-sibs, and resolving such relationships with

genetic markers is fairly straightforward (Jones and Wang

2009). Through molecular tagging of georeferenced sib-

lings, it is thus possible to estimate parameters such as

colony density, foraging distances, or dispersal distances

by queens and males to reveal species-speciﬁc life history

traits and how populations respond to local landscape

conditions (reviewed in Woodard et al. 2015). Kinship

estimates in social insects have most commonly relied on

microsatellite loci, taking advantage of a high degree of

polymorphism to distinguish individual genotypes. How-

ever, microsatellites can have a high degree of genotyping

error and are not ideal for high throughput analysis because

they require substantial time to prepare and genotype

samples, and visually inspect the often noisy genotyping

chromatograms. Studies suggest that despite the reduced

power of individual biallelic SNPs, even a modest number

of markers (e.g., 80–125 SNPs) will have equal or greater

power and accuracy than a standard microsatellite panel for

assessing inbreeding and relatedness (Morin et al. 2009;

Smouse 2010). HTS technologies, together with reduced-

representation sequencing library preparation strategies,

provide a means to rapidly and efﬁciently multiplex tens,

hundreds, or even thousands of individuals for a desired

number of SNP markers. A recently developed modiﬁca-

tion of RADseq that incorporates sequence capture (RAD

capture) to ﬂexibly target subsets of informative markers

(Ali et al. 2016) will allow researchers to reliably genotype

all individuals from an entire study at a sufﬁcient number

of genetic markers for reliable kinship estimation in a

single sequencing run. It remains to be seen, however,

whether HTS-based approaches to determining individual

relatedness will empirically or economically outperform

existing methods in species where microsatellite markers

have already been developed and laboratory pipelines are

in place.

Population structure, phylogeography,

and taxonomy

Population structure

The investigation of population structure and non-random

patterns of dispersal and gene ﬂow has been among the

most directly applicable contributions of molecular popu-

lation genetics to conservation and management decision-

making. Broadly speaking, questions of population struc-

ture can range from delimiting closely related or cryptic

species, identifying evolutionarily signiﬁcant units (ESUs)

within species, to revealing responses of population con-

nectivity to habitat structure or recent anthropogenic

modiﬁcations to the landscape (Hey and Machado 2003).

As emphasized above with respect to genetic diversity,

population genetics studies using traditional markers such

as microsatellites and Sanger sequencing of mitochondrial

or nuclear genes have made signiﬁcant contributions to our

understanding of bee population structure and taxonomy.

Genomic methods should improve resolution of analyses

over more traditional markers through the sheer numbers of

available loci, as it is generally recognized that studies of

one or a few markers will often be insufﬁcient, unreliable

and underpowered for high-resolution analysis of

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123

population history and demography. Furthermore, HTS

approaches like RADseq may provide ﬁner scale resolution

of population structure even with more limited individual

and population sampling (Robinson et al. 2014b; Lozier

et al. 2016; Jeffries et al. 2016).

At the population level, a large number of studies have

investigated intraspeciﬁc gene ﬂow in wild and managed

bees with the goal of understanding how landscape quality

and arrangement, habitat fragmentation, isolation, and

other potential barriers disrupt gene ﬂow in bees. Such

studies have historically included basic tests of population

structure based on differentiation (e.g., F

), isolation-by-

distance, distance-based trees, and genotype clustering

(Danforth et al. 2003; Zayed et al. 2006; Zayed and Packer

2007; Strange et al. 2008; Delaney et al. 2009; Darvill et al.

2010; Lozier et al. 2011). Increasingly, incorporation of

other tools such as geographic information systems and

spatial data have enabled tests of more realistic landscape

genetics models (Manel et al. 2003) to identify environ-

mental factors inﬂuencing historical and contemporary

population structure in diverse solitary and social bees

(Zimmermann et al. 2011; Goulson et al. 2011; Jha and

Kremen 2013; Lozier et al. 2013;Lo

´pez-Uribe et al. 2015;

Dellicour et al. 2016; Jaffe

´et al. 2016). The capacity to

more ﬁnely resolve relationships among individuals and

populations with genomic markers will likely improve the

capacity to test increasingly realistic and complex popu-

lation genetic models, although more work is needed to

understand how spatial and temporal heterogeneity will

inﬂuence genomic data (Epps and Keyghobadi 2015).

Ultimately, understanding spatial patterns of genetic vari-

ation within and among species, and explicitly testing the

factors that impede gene ﬂow at a ﬁne resolution, will

assist conservation through the development of optimal

landscape management practices that aid connectivity in,

for example, heavy agricultural or urban habitats (e.g., Jha

and Kremen 2013) or areas facing deforestation (Jaffe

´et al.

2016).

Taxonomy and cryptic species

At the highest level of population structure, accurate

recognition of species is especially important for conser-

vation, with species being the taxonomic unit of mea-

surement for inclusion on biodiversity lists, for monitoring,

and for regulatory decision making (Mace 2004). Below

the species level however, identiﬁcation of ESUs or man-

agement units will also be crucial, and genomic tools have

a use here as well, especially for deﬁning populations

possessing uniquely adaptive variation (Palsbøll et al.

2007; Funk et al. 2012). For bees, accurate speciﬁc and

intraspeciﬁc taxonomic assessments may be especially

important when species are candidates for domestication

and management (Williams et al. 2012a; Hurtado-Burillo

et al. 2013; Rasmussen 2013). In many bee groups where

morphological characters are limited, taxonomic reassess-

ments will often be required. Molecular methods like

Sanger sequencing of mitochondrial genes (e.g., DNA

barcoding) have proven useful for phylogenetics and spe-

cies hypothesis testing in bees (Williams et al. 2012b;

Danforth et al. 2013; Hurtado-Burillo et al. 2013; Shefﬁeld

et al. 2016). Although multilocus approaches are usually

preferable to overcome reliance on a single gene tree to

infer species histories (Fujita et al. 2012), barcoding should

continue its utility in resolving bee diversity, particularly

when combined with HTS approaches to ‘‘extend’’ the

barcode (Coissac et al. 2016). By providing a tremendous

source of largely independent loci, HTS methods should

provide the greatest beneﬁt to taxonomy when single locus

analyses are uninformative, such as when historical effec-

tive population sizes are large and divergence times shal-

low, as is likely true for many bees.

One of the greatest promises from population genomic

data for population structure analyses will be improved

resolution to detect hybridization and introgression among

species (Hohenlohe et al. 2011). This is particularly relevant

for managed species that are transported outside of their

native ranges, but also for movement among regions within a

species’ range (Lozier et al. 2015). The potential for inter or

intra-speciﬁc hybridization from managed bees into wild

native species is especially concerning (Kanbe et al. 2008;

Duennes et al. 2012), with effects that can include dilution of

locally adapted genetic variation and ‘‘genomic extinction,’’

where ancestral genomes of locally adapted populations are

lost after generations of hybridization (De la Ru

´a et al. 2009;

Byatt et al. 2016). In honey bees for example, management

appears to have enhanced genetic diversity over native wild

lineages (Harpur et al. 2012), although potentially at the risk

of genetic homogenization and loss of locally adapted vari-

ation that could actually hamper populations in the long term

(De La Ru

´a et al. 2013). Genomic tools have great potential

to not only detect and track hybridization with high resolu-

tion but also to track where in the genome introgression is

occurring and providing clues to its functional signiﬁcance.

Indeed, HTS of different honeybee subspecies led to the

creation of an ancestry-informative SNP panel that can be

used to track ancestry and introgression of honey bees

(Chapman et al. 2015; Harpur et al. 2015).

Importantly, massive new datasets will require new

computational and statistical tools for analyzing demo-

graphic history. Species-tree delimitation based approaches

that treat loci independently and do not rely on concate-

nation, including the software SNAPP (Bryant et al. 2012)

or SVDquartets (Chifman and Kubatko 2014) use RADtags

or SNPs datasets to generate well-supported taxonomic

assessments. Large SNP datasets are very powerful for

Conserv Genet

123

estimating migration rates, population sizes, and diver-

gence times, along with testing alternative phylogeographic

scenarios using analyses of the site frequency spectrum

(Gutenkunst et al. 2009; Excofﬁer et al. 2013)or

Approximate Bayesian Computation (Robinson et al.

2014a).

The early stages of population genomic structure analysis

in bees

Despite promising avenues for future research, the appli-

cation of HTS to study population structure and taxonomy

in bees is still in its infancy. The publication of the Apis

mellifera genome made immediate contributions to

resolving challenging questions regarding the complex

evolutionary history of native and managed honey bees by

providing a ﬁrst generation SNP panel for population

genomics analysis (Whitﬁeld et al. 2006). As technology

has advanced, research utilizing whole genome rese-

quencing (i.e. true population genomics) has renewed the

debate on the origins and demographic history of honey

bees at global (Wallberg et al. 2014) and regional (Fuller

et al. 2015) scales. It will be interesting to see the ultimate

resolution of this once all A. mellﬁera subspecies are

sequenced. Outside of Apis, to date there has been limited

application of genomic tools for studies of population

structure in bees. One recent study in bumble bees used

RNAseq and double-digest RADseq data to test the relative

signatures of divergence and admixture in a phenotypically

polymorphic North American bumble bee B. bifarius

(Lozier et al. 2016). Despite microsatellite data indicating

weak genetic structure and possibly ongoing gene ﬂow

among color forms, genomic data clearly indicated a deep

divergence with little evidence for admixture among major

lineages. One possible explanation is that a small number

of microsatellites may have had insufﬁcient power to dis-

tinguish recent divergence from ongoing gene ﬂow,

whereas genome-wide SNP data provided a sufﬁcient

number of genetic markers to clearly delineate population

structure. Results from this work may lead to taxonomic

revision that would have gone unrecognized from other

published data.

An important characteristic of these exemplar studies of

HTS in bees is that the data produced are not only useful

for traditional population structure assessments, but also

provide a means for deeper understanding of evolutionary

genetic processes that are ultimately most important for

conservation and understanding how species respond to

environmental change. For example, honey bee genomic

data not only provides information on the demographic

history of Apis, but perhaps more importantly has begun to

reveal the mutations that underlie adaptive evolution in

honey bees (Zayed and Whitﬁeld 2008; Harpur et al. 2014;

Wallberg et al. 2014). Likewise, by providing polymor-

phisms across coding regions, transcriptome sequencing

can shed light on genetic mechanisms underlying adapta-

tion (Woodard et al. 2011; Pimsler and Lozier pers.

comm.) in addition to informing taxonomy and phylogeny.

Thus, we expect bee population genomics to provide more

‘‘bang for the buck’’ compared to more traditional markers,

where researchers can address questions on diversity and

population structure, as well as gain insights into new

topics of research that could revolutionize conservation

efforts.

Narrow-sense Conservation Genomics Strategies

for Bees

Conservation genomic studies provide useful intrinsic

information about declining populations. For example,

these studies help us answer questions such as: How small

are the populations? Are they isolated? Is there evidence of

bottlenecks? Do they suffer from inbreeding? In additional

to addressing these important questions, genomics can also

be used to both answer extrinsic question about the causes

of species declines and to provide tools for managing the

health of species (Fig. 1b).

‘Omics strategies for monitoring and diagnosing bee

health

Discovering the causes behind species decline is the ﬁrst

step towards proper conservation planning for species

recovery. Although we generally know the ‘usual suspects’

of bee declines—pathogens and disease, habitat loss and

fragmentation, agrochemicals, nutrition and climate

change—these factors are not likely to be all operating at

the same time and are most likely population speciﬁc. It

can thus require years of ﬁeld and lab research before the

factors leading to decline for a speciﬁc population of pol-

linators can be identiﬁed. Even in the honeybee—arguably

the most well studied bee and certainly the species with the

most genomic resources—there is still considerable con-

troversy about why some populations are experiencing high

mortality (Eisenstein 2015).

A major challenge in rapid diagnosis of causal factors in

population decline is the lack of tools for assessing the

health of native and managed bees. Genomics holds great

promise for transforming the ﬁeld of bee conservation by

providing a suite of tools for diagnosing pollinator health.

‘Omic markers are routinely applied in human healthcare,

to provide early predictions of disease susceptibility,

diagnose certain disease such as cancer, and to guide per-

sonalized medicine by, for example, recommending phar-

maceuticals that work best with a patient genotype and

Conserv Genet

123

physiology (Ziegler et al. 2012). We can envision several

applications of ‘omic tools to monitor bee health and

diagnose stressors in the ﬁeld. The basic premise of using

‘omic tools to diagnose bee health rests on the concept that

organisms deal with perturbations in their environment

through behavioral, physiological, or metabolic changes

that are ﬁrst initiated through transcriptional changes. For

example, individuals deal with disease or toxins in the

environment by activating their immune system or detox-

iﬁcation system. If changes in transcriptional states are

closely coupled with changes in the environment, then we

can use knowledge of transcriptional proﬁles to infer the

presence of speciﬁc stressors in the environment. There is a

considerable body of literature showing that transcriptional

proﬁling can accurately predict changes in individual bee

behavior. In the honeybee, almost all behavioral states

investigated so far have been associated with distinct brain

transcriptional states—called neurogenomic states—that

are highly robust and repeatable (Whitﬁeld et al. 2003;

Zayed and Robinson 2012). If transcription can predict

labile traits such as behavior, transcriptional states associ-

ated with a bee’s exposure to perturbations and stressors in

its environment would also be expected.

Developing ‘Omic markers for bee health will require a

systematic effort to study how various ecologically-rele-

vant perturbations (e.g. disease status, nutrition, exposure

to various agrochemicals) inﬂuence transcriptional states of

key tissues (e.g. abdomen tissues for phenotypes associated

with disease, detoxiﬁcation, metabolism and reproduction,

and brain tissue for phenotypes associated with behavior)

from many species across the bee phylogeny. This would

allow researchers to identify and validate biomarkers—

genes with expression patterns that are predictive of

speciﬁc stressors. These biomarkers can be used as part of a

‘ﬁrst-response’ toolkit by quickly highlighting the most

likely stressors that are affecting bee populations targeted

for conservation.

Revealing the genetics underlying traits important

for conservation and management

In addition to providing diagnostic tools, genomics and

HTS have revolutionized the ﬁeld of genetics by providing

a framework for identifying the mutations underlying

complex traits or adaptive evolution in non-model organ-

isms. Traditionally, identifying the genetics underlying a

complex trait required an immense effort and a genetically

tractable model organism. In species where genetic

manipulation is impossible or difﬁcult, it is possible to use

genetic crosses to map broad regions of the genome that

control quantitative traits, but these QTL approaches rarely

yielded information about causal mutations (Hunt et al.

1998). HTS can reveal the genetics underlying interesting

traits by directly associating genomic differences with

phenotypic differences in natural populations without the

need for laboratory crosses–approaches that are broadly

called genome-wide association studies (GWAS). GWAS

are commonly used to study the genetics underlying phe-

notypic differences, including disease susceptibility, in

humans (McCarthy et al. 2008). GWAS rely on whole

genome sequencing of individuals, or very dense geno-

typing to allow of the detection of unobserved casual

mutations through close physical linkage to nearby neutral

mutations. Recombination rates in social bees are very high

(Weinstock et al. 2006; Wilfert et al. 2007; Sadd et al.

2015), which presents a very small target for detecting

causal mutations through linkage with neutral markers. In

bees, GWAS approaches will require whole genome

sequencing or very dense genotyping to work around the

small haplotype blocks expected in natural populations

with high rates of recombination. At the same time, high

recombination rates may ease the identiﬁcation of causal

mutations once genome regions are discovered. Another

challenge to using genome scan approaches like GWAS in

wild bee populations is the role of demographic history in

shaping allele frequencies; population structure and diver-

gence can produce spurious associations between marker

loci and variables of interest when demography is not taken

into account (e.g., Hancock et al. 2011). However, a

number of statistical methods are now available to incor-

porate information on population history, and sampling

schemes can be designed to incorporate the effects of

spatial correlation on allele frequencies to identify outliers

correlated with phenotype or environmental variables (re-

viewed in Lotterhos and Whitlock 2014).

Once candidate loci are identiﬁed through GWAS or

other ‘‘outlier’’ detection approaches, in species where

selective breeding is possible, discovered loci can be used

for marker-assisted selection in breeding programs that

strive to improve heritable traits of interest for management

or conservation. For example, in species that are com-

mercially reared for pollination services, it will be possible

to selectively breed disease-resistant genotypes by select-

ing on mutations that inﬂuence innate or social immunity.

Such research is currently underway in honey bees, where

GWAS is being used to identify genetic markers linked to

variation in a suite of economically valuable traits across

hundreds of colonies (Foster and Zayed, personal com-

munication). When genetic rescue of wild populations

(Frankham 2015) is a goal, loci identiﬁed as adaptive (e.g.,

correlated with a phenotypic trait or environmental varia-

tion) or otherwise marking distinct evolutionarily signiﬁ-

cant units can be used to select optimal source populations

for reintroductions.

Conserv Genet

123

Beyond the bee: HTS insights for conservation

from bee-associated organisms

A characteristic of HTS approaches is that any molecule of

DNA in a sequencing library has a chance of being

sequenced in proportion to its abundance. This can present

an obvious problem of ‘‘wasted’’ sequence reads if the

DNA isolate from the target organism is diluted with DNA

from other organisms. In most cases this is to be avoided,

however these extra-organismal reads have some potential

to provide valuable secondary information for bee con-

servation. Stray sequencing reads from DNA and RNA

HTS studies have the potential to reveal infections with

previously unrecognized bacteria, fungi, viruses, and other

microorganisms. For example, deep sequencing of RNA

from honey bee isolates has been used to reveal infections

both with known microorganisms as well as novel viruses

(Runckel et al. 2011). Similarly, ‘stray’ DNA sequences

found within the Bombus impatiens genome were used to

describe the genome of a bacterial symbiont Schmid-

hempelia (Martinson et al. 2014). DNA from pollen will

likely be found in many isolates from foraging bees, and

could thus be used to determine foraging preferences

among species or geographic regions. Thus, querying

unmapped reads from a sequencing experiment against

available genome databases could potentially prove to be a

valuable exercise.

Genomic approaches have more immediate and direct

utility for targeted analysis of known disease causing

organisms, parasites and pathogens. For example, HTS has

facilitated sequencing of RNA viruses in honey bees that

provide preliminary, but previously hidden, information on

the evolutionary patterns of dispersal and selection in these

potentially damaging organisms (Cornman et al. 2013a).

High-throughput sequencing studies of honey bee viruses

have detected recombination among viral strains, providing

insights into the evolution of novel, and potentially more

virulent, pathogen genotypes (Moore et al. 2011; Ryabov

et al. 2014; McMahon et al. 2016). Outside of viruses, the

genomes of the important honey bee parasites Nosema

ceranae and Nosema apis have been sequenced (Cornman

et al. 2009; Chen et al. 2013), which should contribute to

improved resolution to track the history of these parasites

with respect to that of their hosts (e.g., Maside et al. 2015).

In a recent analysis of the bumble bee parasite Nosema

bombi (Microsporidia), which is suspected of being inva-

sive in North America and playing a role in some bumble

bee declines, Cameron et al. (2016) used deep amplicon

sequencing of Nosema rRNA and genome reduction tech-

niques to test whether Nosema in North America could

represent an invasive strain. No signiﬁcant differentiation

between European and North American isolates was found,

but the data suggested low levels of genetic variation in

general. Although phylogeographic results were somewhat

ambiguous, in the near future we expect whole genome

sequencing of pathogens (i.e. parasite population geno-

mics) to become a feasible strategy for resolving the ori-

gins of N. bombi in North America, as well as for other

parasites and pathogens that are threatening native bees as

domesticated species are transported globally (Goulson and

Hughes 2015). Furthermore, whole genome studies will be

necessary for uncovering genetic variation that correlates

with different functional aspects of host-parasite interac-

tions, including variation in virulence, growth, and trans-

mission (McMahon et al. 2016). As genomic data from

parasites and pathogens accumulate, the development of

diagnostic strategies to detect both species and functional

strain variants will become increasingly plausible.

Finally, community proﬁling of microbial or pollen

communities isolated from bees will also be a valuable

contribution of genomic methods for bee conservation

through improved understanding of foraging and nutrition.

For example, Richardson et al. (2015) applied HTS bar-

coding of the ITS2 region to obtain qualitative and quan-

titative proﬁles of pollen foraging by honey bees in an

agricultural landscape. Such methods should be easily

extended to wild bees in natural settings provided a sufﬁ-

cient reference sequence database can be generated (Keller

et al. 2015). Proﬁling microbial communities associated

with bees (the ‘‘microbiome’’) using 16S rRNA amplicon

sequencing has similarly gained increased attention in

recent years (Lim et al. 2015; Moran 2015), and is begin-

ning to illuminate the relationship between the microbiome

and bee health in different species (Koch and Schmid-

Hempel 2011). Metagenomic studies will ultimately tell us

what functions bacterial communities are providing for

their hosts (Engel et al. 2012).

Sampling concerns for conservation genomics

of bees

A shift from PCR-based molecular techniques will require

parallel shifts in sample collection, handling, preservation,

and processing. Most whole genome approaches usually

require several micrograms of DNA of moderate quality

(short read sequencing is somewhat robust to shearing of

DNA molecules during extraction), while single strand

sequencing approaches that generate very long reads (e.g.

PacBio) are particularly sensitive to sample quality and

isolation method. The latter approaches are most useful for

de novo sequencing, but for most population genomics re-

sequencing studies, shorter-read length technologies will

be sufﬁcient. Nevertheless, all HTS methods beneﬁt from

high molecular weight DNA that is free of contamination

(i.e., a single high molecular weight band with minimal

Conserv Genet

123

smearing on an agarose gel)(e.g., see Graham et al. 2015

for RADseq evaluation). Genome reduction techniques still

require a considerable amount of DNA, and some RADseq

protocols suggest a sample of *1lg of non-degraded of

genomic DNA at 25 ng/lL (Etter et al. 2011), although

many approaches will work with less material.

For DNA-based methods, we have had success with

preserving whole samples directly into pure ethanol and

maintained on ice or dry ice in the ﬁeld, with storage at

-80 °C in the laboratory. For enzymatic approaches like

RADseq, even weak DNA degradation may reduce library

quality (Lozier personal observation). RNAseq will be the

most demanding technology with respect to sample integrity

(Gayral et al. 2011), requiring specimens be rapidly killed

and preserved cryogenically without thawing until RNA

isolation, although chemical preservatives can maintain

RNA integrity in bees under ﬁeld conditions (Lozier et al.

2016). Careful consideration of tissues used in isolation may

also be important for both DNA and RNA, as certain tissues

may harbor contaminating microorganisms or plant material

that can reduce sequencing coverage for the target indi-

vidual. Typically, thoracic muscle tissue provides the

highest quality DNA, and is largely free of contaminants.

Thus, many HTS approaches may be challenging for older

pinned specimens that are commonly available for many

bees. Moreover, conservation genetics studies of bees often

rely on non-lethal sampling to avoid negative impacts on

wild populations (e.g., tarsal clips) (Holehouse et al. 2003).

Such approaches work well for PCR-based molecular

markers, but may not produce sufﬁcient DNA for many HTS

methods. Recent advances in techniques that incorporate a

target capture step may help overcome such challenges

(Suchan et al. 2016). In cases where lethal collection is

required to obtain sufﬁcient DNA, researchers will neces-

sarily have to balance the beneﬁts achieved from conducting

the study against negatively impacting the populations in

need of conservation. Encouragingly, however, recent

studies suggest that even fairly intensive collections of bees

have little impact on species diversity over time (Gezon et al.

2015). This is likely to be especially true for social species

like bumble bees where a reasonable population sample of

workers (*20–25 individuals) may contain only 1–2 bees

per colony on average (Cameron et al. 2011). Thus, except

for the most threatened taxa, low levels of lethal sampling

should not have substantial negative impacts on many pol-

linators, although we encourage researchers to make the

greatest use of killed specimens beyond genotyping alone

(e.g., imaging, morphological analysis, pathogen screening).

One ﬁnal caveat regarding sampling

Correct taxonomic identiﬁcation of target species may be

even more important for HTS than other molecular studies.

With larger numbers of loci, and typically smaller numbers

of individuals in population genomics, incorporating

sequences from mis-identiﬁed individuals will likely con-

tribute to spurious population genetics summary statistics,

which will be especially problematic in Pool-seq studies.

Studies of species belonging to cryptic morphological

groups should explicitly document species identiﬁcation

approaches, and where necessary should use molecular

conﬁrmation against a known reference database (e.g.,

DNA barcoding) prior to spending time, effort and funds

on HTS of the wrong species.

Concluding statements and future directions

Considering the reductions in cost of HTS and access to

public platforms for genome assembly and gene predic-

tions, and analysis (Fuller et al. 2015), we anticipate the

publication of a plethora of bee genomes over the next

decade. Notably, new single strand sequencing technolo-

gies are expected to substantially increase the quality of de

novo assembly of new genomes. Effort should be made to

sequence representative genomes across the major bee

tribes, especially within short-tongued bees, which are

currently under-represented. Moreover, sequencing species

with a broader range of demographic histories, including

both stable species and species of conservation concern,

may help elucidate genetic factors associated with popu-

lation declines. Although HTS studies of stable and

declining bee species have been conducted (Lozier 2014),

we are aware of only a single whole genome sequencing

project in bee species targeted for conservation: the yellow-

banded bumble bee, B. terricola, (Kent, Dey, Colla, and

Zayed, per. comm.), which is declining in parts of its range

(Colla and Packer 2008; Cameron et al. 2011). In addition

to focusing on demographic comparisons, sequencing

genomes of bees across life-history gradients (e.g. diet

specialists vs. diet generalist; solitary vs. semi-social vs.

social) may further help identify genomic features associ-

ated with differing life-history traits and their relationship

to the susceptibility of bees to anthropogenic disturbances.

In summary, we think that genomics holds great promise

for transforming the ﬁeld of bee conservation, in the same

way that it has transformed other ﬁelds of biology. Geno-

mics will provide bee biologists with better tools to esti-

mate important demographic parameters of relevance to

species conservation, in addition to providing novel ways

for assessing the health of pollinators and for improving

pollinator health using ‘omic-assisted selective breeding.

Given concerns that conservation genomics is currently an

academic discipline that has yet to make major break-

throughs for applied conservation (Shafer et al. 2015), it

will be important for bee researchers to connect and

Conserv Genet

123

communicate results to the broader community, including

commercial breeders and beekeepers, farmers, land man-

agers, and policy makers. As a group, bees are well suited

to highlight the power of genomics in conservation biol-

ogy; they are crucially important pollinators of native

plants and agricultural crops, they face serious threats in

both managed and natural settings, they capture public

attention as charismatic microfauna, their often small

genomes make them particularly feasible for HTS studies,

and, importantly, many communication networks already

exist for translating research results into application. As an

example relating to wild bee populations, a framework

exists to directly incorporate genetic information into

conservation strategies for bumble bees through the Inter-

national Union for the Conservation of Nature Bumblebee

Specialists Group’s Conservation Genomics committee,

which can directly communicate ﬁndings from basic

genomic research to a broad conservation-minded audi-

ence. We have discussed just a few simple examples of the

ways in which genomic tools might help advance bee

conservation, and we imagine that this ﬁeld will undergo

considerable acceleration in the coming years. Several

studies are underway in our labs, for example, to simulta-

neously investigate gene ﬂow, diversity, and local adapta-

tion in several bumble bee species using diverse genomic

tools (i.e. both broad and narrow-sense conservation

genomics) that will be directly relevant to conservation and

domestication efforts. While it was the charismatic chee-

tahs and wolves that ﬁrst demonstrated the importance of

genetics to conservation, we think that bees have great

potential to showcase the importance of genomics in

applied conservation.

Acknowledgments We thank the Natural Sciences and Engineering

Council of Canada (Discovery grant to AZ) and the United States

National Science Foundation Division of Environmental Biology

(DEB-1457645 to JDL) for funding ongoing work relating to con-

servation genomics of bees. We thank S Jha, M Lopez-Uribe, and A

Soro for organizing this special issue on Bee Conservation Genetics

and the 2015 Ecological Society of America symposium bearing the

same title.

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Conservation genomics analysis reveals recent population decline and possible causes in bumblebee Bombus opulentus

Article

Jan 2024
INSECT SCI

Bumblebees are a genus of pollinators ( Bombus ) that play important roles in natural ecosystem and agricultural production. Several bumblebee species have been recorded as under population decline, and the proportion of species experiencing population decline within subgenus Thoracobombus is higher than average. Bombus opulentus is 1 species in Thoracobombus , but little is known about its recent population dynamics. Here, we employed conservation genomics methods to investigate the population dynamics of B . opulentus during the recent past and identify the likely environmental factors that may cause population decline. Firstly, we placed the scaffold‐level of B . opulentus reference genome sequence onto chromosome‐level using Hi‐C technique. Then, based on this reference genome and whole‐genome resequencing data for 51 B . opulentus samples, we reconstructed the population structure and effective population size ( N e ) trajectories of B . opulentus and identified genes that were under positive selection. Our results revealed that the collected B . opulentus samples could be divided into 2 populations, and 1 of them experienced a recent population decline; the declining population also exhibited lower genetic diversity and higher inbreeding levels. Genes related to high‐temperature tolerance, immune response, and detoxication showed signals of positive selection in the declining population, suggesting that climate warming and pathogen/pesticide exposures may contribute to the decline of this B . opulentus population. Taken together, our study provided insights into the demography of B . opulentus populations and highlighted that populations of the same bumblebee species could have contrasting N e trajectories and population decline could be caused by a combination of various stressors.

The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics

Article

Full-text available

Jun 2024
BMC GENOMICS

Background The field of bee genomics has considerably advanced in recent years, however, the most diverse group of honey producers on the planet, the stingless bees, are still largely neglected. In fact, only eleven of the ~ 600 described stingless bee species have been sequenced, and only three using a long-read (LR) sequencing technology. Here, we sequenced the nuclear and mitochondrial genomes of the most common, widespread and broadly reared stingless bee in Brazil and other neotropical countries—Tetragonisca angustula (popularly known in Brazil as jataí). Results A total of 48.01 Gb of DNA data were generated, including 2.31 Gb of Pacific Bioscience HiFi reads and 45.70 Gb of Illumina short reads (SRs). Our preferred assembly comprised 683 contigs encompassing 284.49 Mb, 62.84 Mb of which (22.09%) corresponded to 445,793 repetitive elements. N50, L50 and complete BUSCOs reached 1.02 Mb, 91 contigs and 97.1%, respectively. We predicted that the genome of T. angustula comprises 17,459 protein-coding genes and 4,108 non-coding RNAs. The mitogenome consisted of 17,410 bp, and all 37 genes were found to be on the positive strand, an unusual feature among bees. A phylogenomic analysis of 26 hymenopteran species revealed that six odorant receptor orthogroups of T. angustula were found to be experiencing rapid evolution, four of them undergoing significant contractions. Conclusions Here, we provided the first nuclear and mitochondrial genome assemblies for the ecologically and economically important T. angustula, the fourth stingless bee species to be sequenced with LR technology thus far. We demonstrated that even relatively small amounts of LR data in combination with sufficient SR data can yield high-quality genome assemblies for bees.

Distinct genome architecture underlies fine-scale population differentiation in two common European bumblebees ( Bombus pascuorum and Bombus lapidarius )

Preprint

Full-text available

May 2024

Bumblebees are keystone pollinators which facilitate the reproduction of a wide range of wild and agricultural plants. Their abundance and diversity have been severely reduced by anthropogenic stressors such as land-use change and widespread habitat fragmentation. However, we lack a comprehensive understanding of bumblebee population structure and local adaptation in response to human-altered landscapes. We here discover surprisingly fine-scaled population structure (e.g. ~300km) within two widely occurring bumblebee species, Bombus lapidarius and Bombus pascuorum, by analysing whole genome data of 106 specimens from 7 sites in Northern Europe. Our sample range encompasses a mosaic of land-use types with varying levels of habitat fragmentation and natural oceanic barriers. While the observed population structure is largely associated with reduced gene flow across natural barriers, we also detect significant divergence between populations sampled from more fragmented, agricultural landscapes. Furthermore, we identify species-specific patterns of population structure which are underpinned by distinct genomic architecture. Whereas genetic divergence in B. lapidarius is spread relatively evenly across the genome, divergence in B. pascuorum is concentrated within several megabase-sized genomic regions with significantly elevated differentiation, including a putative chromosomal inversion, which may underlie well-known colour polymorphisms across its range. Our observations reveal unexpectedly high levels of inter- and intraspecific genomic diversity within the bumblebee genus, and highlight the necessity of increasing our understanding of bumblebee population structure and connectivity to design optimal bumblebee conservation strategies.

Genomic variation in montane bumblebees in Scandinavia: High levels of intraspecific diversity despite population vulnerability

Article

Full-text available

Dec 2023

Populations of many bumblebee species are declining, with distributions shifting northwards to track suitable climates. Climate change is considered a major contributing factor. Arctic species are particularly vulnerable as they cannot shift further north, making assessment of their population viability important. Analysis of levels of whole‐genome variation is a powerful way to analyse population declines and fragmentation. Here, we use genome sequencing to analyse genetic variation in seven species of bumblebee from the Scandinavian mountains, including two classified as vulnerable. We sequenced 333 samples from across the ranges of these species in Sweden. Estimates of effective population size ( N E ) vary from ~55,000 for species with restricted high alpine distributions to 220,000 for more widespread species. Population fragmentation is generally very low or undetectable over large distances in the mountains, suggesting an absence of barriers to gene flow. The relatively high N E and low population structure indicate that none of the species are at immediate risk of negative genetic effects caused by high levels of genetic drift. However, reconstruction of historical fluctuations in N E indicates that the arctic specialist species Bombus hyperboreus has experienced population declines since the last ice age and we detected one highly inbred diploid male of this species close to the southern limit of its range, potentially indicating elevated genetic load. Although the levels of genetic variation in montane bumblebee populations are currently relatively high, their ranges are predicted to shrink drastically due to the effects of climate change and monitoring is essential to detect future population declines.

Global governance for digital sequence information on genetic resources: Demand, progress and reforming paths

Article

Full-text available

Mar 2023

The cross‐border transmission of digital sequence information (DSI) on genetic resources is an emerging global governance issue, particularly since its inclusion in the post‐2020 framework of the Convention on Biological Diversity. Based on a brief review of the value of DSI and the need for global governance, this paper identifies three elemental regimes on ‘physical’ genetic resources that are in conflict: divergent principles of sovereignty claim, global multilateral sharing and intellectual property rights protection. It then traces the progress of each elemental regime on DSI and describes their ongoing conflicts. Two reform strategies for better governance are suggested: one gradual and path‐dependent and one more radical. The basis of the radical strategy is to promote labour division and cooperation among institutions of different elemental regimes within a three‐layered system of DSI values.

Comparative cytogenetic analysis reveals chromosomal variability in five stingless bees of the genus Trigona (Apidae, Apinae, Meliponini)

Article

Full-text available

Mar 2023

The stingless bee genus Trigona includes 32 species, exclusive to the New World, which are grouped into two clades (A and B) according to phylogenetic molecular data. Cytogenetic studies have been performed in only seven Trigona taxa, and molecular cytogenetic data are available for only one species. These studies have been important for the chromosomal characterization of the species; however, discussions focusing on the karyotype evolution of Trigona in a phylogenetic context are lacking. In this study, we characterized the karyotype, through classical and molecular cytogenetics, of five Trigona species: T. pallens and T. williana, from clade A, and T. hypogea, T. aff. fuscipennis, and T. truculenta, from clade B, in order to provide insights into the karyotype evolution in Trigona and investigate whether the analyzed cytogenetic markers may have a phylogenetic signal. All five Trigona species have 2n = 34 chromosomes. Variations in the karyotype formula were observed in T. truculenta and T. hypogea compared with the other three species. Although heterochromatin distribution was restricted to one of the arms in most of the chromosomes of the five species, C-banding experiments highlighted a lower degree of heterochromatin compaction in T. pallens and T. williana. The microsatellite (GA)15 was exclusively located in the euchromatic regions of the chromosomes in all five species. The number of pairs bearing rDNA genes varied among the species studied, and this cytogenetic trait seems to reflect the phylogeny, separating the species into two clades. This study showed interspecific variations to a greater or lesser degree among Trigona species, highlighting the intense chromosomal evolutionary dynamics in the genus.

Range-wide genetic analysis of an endangered bumble bee (Bombus affinis, Hymenoptera: Apidae) reveals population structure, isolation by distance, and low colony abundance

Article

Mar 2024
J INSECT SCI

Declines in bumble bee species range and abundances are documented across multiple continents and have prompted the need for research to aid species recovery and conservation. The rusty patched bumble bee (Bombus affinis) is the first federally listed bumble bee species in North America. We conducted a range-wide population genetics study of B. affinis from across all extant conservation units to inform conservation efforts. To understand the species’ vulnerability and help establish recovery targets, we examined population structure, patterns of genetic diversity, and population differentiation. Additionally, we conducted a site-level analysis of colony abundance to inform prioritizing areas for conservation, translocation, and other recovery actions. We find substantial evidence of population structuring along an east-to-west gradient. Putative populations show evidence of isolation by distance, high inbreeding coefficients, and a range-wide male diploidy rate of ~15%. Our results suggest the Appalachians represent a genetically distinct cluster with high levels of private alleles and substantial differentiation from the rest of the extant range. Site-level analyses suggest low colony abundance estimates for B. affinis compared to similar datasets of stable, co-occurring species. These results lend genetic support to trends from observational studies, suggesting that B. affinis has undergone a recent decline and exhibit substantial spatial structure. The low colony abundances observed here suggest caution in overinterpreting the stability of populations even where B. affinis is reliably detected interannually. These results help delineate informed management units, provide context for the potential risks of translocation programs, and help set clear recovery targets for this and other threatened bumble bee species.

Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

Article

Sep 2023

Studies of species that experience environmental heterogeneity across their distributions have become an important tool for understanding mechanisms of adaptation and predicting responses to climate change. We examine population structure, demographic history and environmentally associated genomic variation in Bombus vosnesenskii , a common bumble bee in the western USA, using whole genome resequencing of populations distributed across a broad range of latitudes and elevations. We find that B. vosnesenskii exhibits minimal population structure and weak isolation by distance, confirming results from previous studies using other molecular marker types. Similarly, demographic analyses with Sequentially Markovian Coalescent models suggest that minimal population structure may have persisted since the last interglacial period, with genomes from different parts of the species range showing similar historical effective population size trajectories and relatively small fluctuations through time. Redundancy analysis revealed a small amount of genomic variation explained by bioclimatic variables. Environmental association analysis with latent factor mixed modelling (LFMM2) identified few outlier loci that were sparsely distributed throughout the genome and although a few putative signatures of selective sweeps were identified, none encompassed particularly large numbers of loci. Some outlier loci were in genes with known regulatory relationships, suggesting the possibility of weak selection, although compared with other species examined with similar approaches, evidence for extensive local adaptation signatures in the genome was relatively weak. Overall, results indicate B. vosnesenskii is an example of a generalist with a high degree of flexibility in its environmental requirements that may ultimately benefit the species under periods of climate change.

Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes

Article

Full-text available

Sep 2023

Unraveling molecular mechanisms of adaptation to complex environments is crucial to understanding tolerance of abiotic pressures and responses to climatic change. Epigenetic variation is increasingly recognized as a mechanism that can facilitate rapid responses to changing environmental cues. To investigate variation in genetic and epigenetic diversity at spatial and thermal extremes, we use whole genome and methylome sequencing to generate a high-resolution map of DNA methylation in the bumble bee Bombus vosnesenskii . We sample two populations representing spatial and environmental range extremes (a warm southern low-elevation site and a cold northern high-elevation site) previously shown to exhibit differences in thermal tolerance and determine positions in the genome that are consistently and variably methylated across samples. Bisulfite sequencing reveals methylation characteristics similar to other arthropods, with low global CpG methylation but high methylation concentrated in gene bodies and in genome regions with low nucleotide diversity. Differentially methylated sites (n = 2066) were largely hypomethylated in the northern high-elevation population but not related to local sequence differentiation. The concentration of methylated and differentially methylated sites in exons and putative promoter regions suggests a possible role in gene regulation, and this high-resolution analysis of intraspecific epigenetic variation in wild Bombus suggests that the function of methylation in niche adaptation would be worth further investigation.

Constitutive and variable patterns of genome-wide DNA methylation in populations from spatial-environmental range extremes of the bumble bee Bombus vosnesenskii

Preprint

Full-text available

May 2023

Unraveling molecular mechanisms of adaptation to complex environments is crucial to understanding tolerance of abiotic pressures and responses to climatic change. Epigenetic variation is increasingly recognized as a mechanism that can facilitate rapid responses to changing environmental cues. To investigate variation in genetic and epigenetic diversity at spatial and thermal extremes, we use whole genome and methylome sequencing to generate a high-resolution map of DNA methylation in the bumble bee Bombus vosnesenskii . We sample two populations representing spatial and environmental range extremes (a warm southern low-elevation site and a cold northern high-elevation site) previously shown to exhibit differences in thermal tolerance and determine positions in the genome that are constitutively and variably methylated across samples. Bisulfite sequencing reveals methylation characteristics similar to other arthropods, with low global CpG methylation but high methylation concentrated in gene bodies and in genome regions with low nucleotide diversity. Differentially methylated sites (n = 2,066) were largely hypomethylated in the northern high-elevation population but not related to local sequence differentiation. The concentration of methylated and differentially methylated sites in exons and putative promoter regions suggests a possible role in gene regulation, and this high-resolution analysis of intraspecific epigenetic variation in wild Bombus suggests that the function of methylation in niche adaptation would be worth further investigation.

Elevated virulence of an emerging viral genotype as a driver of honeybee loss

Article

Full-text available

Jun 2016
Proc Biol Sci

Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.

Ecological niche modelling and coalescent simulations to explore the recent geographical range history of five widespread bumblebee species in Europe

Article

Full-text available

Jun 2017

Aim Studying the changes in species ranges during the last glaciation event is an important step towards the understanding of the observed patterns of intra‐specific genetic variability. We focused on bumblebees, an interesting biological model to address these questions because cold‐adapted species are likely to have experienced different geographical range histories during the last glacial period compared to more commonly studied, strictly temperate, species. We investigated and compared historical hypotheses regarding the geographical range of five common and co‐distributed West Palaearctic bumblebee species. Location Europe, West Palaearctic. Methods For each species, we inferred present and past (Last Glacial Maximum) distributions from species occurrence records, and present and past climatic data, using the ecological niche modelling (ENM) approach implemented in Maxent . Based on genetic data previously obtained from the sequencing of three gene fragments (mitochondrial locus COI and two nuclear loci EF‐1α and PEPCK ), we then compared global and local patterns of genetic variation using several summary statistics as well as a visual mapping of genetic variation. Finally, we used a spatially explicit model of DNA sequence coalescence to test and compare four evolutionary scenarios derived from ENM results and patterns of genetic diversity. Results Ecological niche modelling results based on climatic data clearly suggested a range continuum in Europe during the last glaciation. Yet, the related evolutionary scenario involving such continuum was less supported than alternative scenarios involving a more fragmented distribution. Indeed, for the three out of five species for which genetic data allowed discriminating among tested scenarios, the scenario that included a fragmented range during the last glaciation was identified as the most likely. Main conclusions Although ENM suggested that bumblebees would have maintained a range continuum across Europe during the last glaciation, coalescent simulations tended to refute the persistence of a large range continuum for these species during this period. This suggests that even for cold‐adapted species, the cooling periods have significantly shrunk and fragmented their respective ranges.

The genomes of two key bumblebee species with primitive eusocial organization

Article

Full-text available

Apr 2015

The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation.

Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L

Article

Full-text available

Mar 2016
MOL ECOL

The conservation of threatened species must be underpinned by phylogeographic knowledge. This need is epitomised by the freshwater fish Carassius carassius, which is in decline across much of its European range. Restriction site associated DNA sequencing (RADseq) is increasingly used for such applications, however RADseq is expensive, and limitations on sample number must be weighed against the benefit of large numbers of markers. This trade-off has previously been examined using simulation studies, however, empirical comparisons between these markers, especially in a phylogeographic context, are lacking. Here, we compare the results from microsatellites and RADseq for the phylogeography of C. carassius to test whether it is more advantageous to genotype fewer markers (microsatellites) in many samples, or many markers (SNPs) in fewer samples. These datasets, along with data from the mitochondrial cytochrome b gene, agree on broad phylogeographic patterns; showing the existence of two previously unidentified C. carassius lineages in Europe; one found throughout northern and central-eastern European drainages, and a second almost exclusively confined to the Danubian catchment. These lineages have been isolated for approximately 2.15 M years, and should be considered separate conservation units. RADseq recovered finer population structure and stronger patterns of IBD than microsatellites, despite including only 17.6% of samples (38% of populations and 52% of samples per population). RADseq was also used along with Approximate Bayesian Computation to show that the postglacial colonisation routes of C. carassius differ from the general patterns of freshwater fish in Europe, likely as a result of their distinctive ecology. This article is protected by copyright. All rights reserved.

Biogeography and designatable units of Bombus occidentalis Greene and B. terricola Kirby (Hymenoptera: Apidae) with implications for conservation status assessments

Article

Full-text available

Apr 2016
J INSECT CONSERV

Conservation action for species of concern requires that “designatable units” (e.g., species, subspecies, geographic races, genetically distinct forms) are clearly defined, or that the species complex is treated as a whole. Several species of bumble bee are currently threatened, and some of these have cryptic colouration (resembling other species), or form complexes that vary considerably in colour patterning. Here we address the taxonomy and distribution of Bombus occidentalis Greene and B. terricola Kirby, both of which are currently of conservation concern in North America. Bombus occidentalis includes two apparently monophyletic groups of COI barcode haplotypes (recently considered as subspecies) with ranges mostly separated by that of their sister species, B. terricola. The southern B. o. occidentalis ranges throughout the western United States and into western Canada from southern Saskatchewan and Alberta, and throughout British Columbia north to ca. 55°N; the northern B. o. mckayi Ashmead, is restricted to north of this in British Columbia, westernmost Northwest Territories, Yukon Territory and Alaska. Bombus o. mckayi exists, as far as is known, only with a “banded” colour pattern. By contrast, B. o. occidentalis occurs in both banded and non-banded colour patterns, although the southern banded colour pattern is geographically isolated from the northern subspecies. Bombus o. occidentalis has declined throughout its range, perhaps due in part to exposure to novel parasites. Despite having similar levels of parasitism (ca. 40 %) as the southern subspecies, B. o. mckayi appears to have stable populations at present. There is therefore compelling evidence that the two subspecies should be distinguished for conservation and management purposes. We present the evidence for their distinction and provide tools for subspecies recognition.

Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly

Article

Jun 2016

Four main evolutionary lineages of A. mellifera have been described including eastern Europe (C) and western and northern Europe (M). Many apiculturists prefer bees from the C lineage due to their docility and high productivity. In France, the routine importation of bees from the C lineage has resulted in the widespread admixture of bees from the M lineage. The haplodiploid nature of the honeybee Apis mellifera, and its small genome size, permits affordable and extensive genomics studies. As a pilot study of a larger project to characterise French honeybee populations, we sequenced 60 drones sampled from two commercial populations managed for the production of honey and royal jelly. Results indicate a C lineage origin, whilst mitochondrial analysis suggests two drones originated from the O lineage. Analysis of heterozygous SNPs identified potential copy number variants near to genes encoding odorant binding proteins and several cytochrome P450 genes. Signatures of selection were detected using the hapFLK haplotype-based method, revealing several regions under putative selection for royal jelly production. The framework developed during this study will be applied to a broader sampling regime, allowing the genetic diversity of French honeybees to be characterised in detail.

Test of the invasive pathogen hypothesis of bumble bee decline in North America

Article

Apr 2016

Significance Wild bumble bees are experiencing population declines globally. Causes of declines in North American populations are unclear, although declining species are more frequently infected by the pathogen Nosema bombi . A widely accepted hypothesis suggests that contact with European species during domestication led to the introduction of exotic N. bombi . By screening museum specimens, we show that N. bombi prevalence increased significantly in declining species in the early to mid-1990s, coincident with N. bombi outbreaks in North American commercial stocks. There is no evidence that exotic Nosema strains were introduced from Europe. Regardless of geographic origins, the temporal connection between N. bombi epizootics in commercial Bombus stocks and increases in wild populations suggests a substantial risk of pathogen transmission with domestication.

High levels of miticides and systemic agrochemicals in North American beehives: Implications for honey bee health

Article

Mar 2010

From barcodes to genomes: Extending the concept of DNA barcoding

Article

Jan 2016
MOL ECOL

DNA barcoding has had a major impact on biodiversity science. The elegant simplicity of establishing massive scale databases for a few barcode loci is continuing to change our understanding of species diversity patterns, and continues to enhance human abilities to distinguish among species. Capitalising on the developments of next generation sequencing technologies and decreasing costs of genome sequencing, there is now the opportunity for the DNA barcoding concept to be extended to new kinds of genomic data. We illustrate the benefits and capacity to do this, and also note the constraints and barriers to overcome before it is truly scalable. We advocate a twin track approach: (i) continuation and acceleration of global efforts to build the DNA barcode reference library of life on earth using standard DNA barcodes, and (ii) active development and application of extended DNA barcodes using genome skimming to augment the standard barcoding approach. This article is protected by copyright. All rights reserved.

Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect

Article

Jan 2016

Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble bee Bombus bifarius comprises two geographically disparate color groups characterized by red-banded and black-banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed that B. bifarius in the USA are structured into two major groups concordant with geography and color pattern, but also suggest ongoing gene flow among regional populations. In this study, we better resolve the relationships among major color groups to better understand evolutionary mechanisms promoting and maintaining such polymorphism. We analyze >90,000 and >25,000 single-nucleotide polymorphisms derived from transcriptome (RNAseq) and double digest restriction site associated DNA sequencing (ddRAD), respectively, in representative samples from spatial and color pattern extremes in B. bifarius as well as phenotypic and geographic intermediates. Both ddRAD and RNAseq data illustrate substantial genome-wide differentiation of the red-banded (eastern) color form from both black-banded (western) and intermediate (central) phenotypes and negligible differentiation among the latter populations, with no obvious admixture among bees from the two major lineages. Results thus indicate much stronger background differentiation among B. bifarius lineages than expected, highlighting potential challenges for revealing loci underlying color polymorphism from population genetic data alone. These findings will have significance for resolving taxonomic confusion in this species and in future efforts to investigate color-pattern evolution in B. bifarius and other polymorphic bumble bee species.

Bee conservation in the age of genomics

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