Population-level Genetic Diversity Research Articles

Anthropogenic and natural disturbances increase local genetic diversity in an early spring geophyte (Ficaria verna Huds)

AbstractThe tetraploid Ficaria verna is a common spring geophyte in central Europe and is considered invasive in the USA and Canada. It is considered an almost seed‐sterile taxon, relying on vegetative reproduction by underground tubers and aerial bulbils. Recent studies have revealed high levels of population genetic diversity in F. verna, raising the question of how genetic diversity is maintained and which factors may be responsible for the observed patterns. Polymorphic nuclear microsatellite markers were established to define multi‐locus genotypes (MLGs), to analyze fine‐scale spatial genetic structure (SGS) using grid and cross‐sampling schemes, and to quantify genetic diversity within and between nine populations with different disturbance regimes in central Germany. In total, 115 MLGs were identified among a total of 347 samples. The G/N ratio varied between 0.16 and 0.70 among populations, and in each population several unique MLGs occurred. Genotypes were highly intermingled within populations, suggesting a “guerrilla” dispersal strategy. Significant SGS (negative regression slope of kinship coefficients against inter‐individual distances) was found in four out of nine populations in fine‐scale cross‐sampling (up to 4 m) and in only one population in grid sampling (up to 14.6 m). No single MLG was found in more than one population, while many alleles were shared between populations. Within‐population clonal and allelic diversity increased with greater exposure to both anthropogenic and natural disturbances. Regular gap openings, facilitated propagule establishment, and propagule dispersal by water and mowing machines are likely important factors explaining the positive effects of disturbance on local genetic diversity of F. verna.

Mussels Propagated from a Single Broodstock Female Retain Most Population-Level Genetic Variation but Have Altered Genetic Structure

Mussels Propagated from a Single Broodstock Female Retain Most Population-Level Genetic Variation but Have Altered Genetic Structure

First Insights into Population Structure and Genetic Diversity Versus Host Specificity in Trypanorhynch Tapeworms Using Multiplexed Shotgun Genotyping.

Theory predicts relaxed host specificity and high host vagility should contribute to reduced genetic structure in parasites while strict host specificity and low host vagility should increase genetic structure. Though these predictions are intuitive, they have never been explicitly tested in a population genomic framework. Trypanorhynch tapeworms, which parasitize sharks and rays (elasmobranchs) as definitive hosts, are the only order of elasmobranch tapeworms that exhibit considerable variability in their definitive host specificity. This allows for unique combinations of host use and geographic range, making trypanorhynchs ideal candidates for studying how these traits influence population-level structure and genetic diversity. Multiplexed shotgun genotyping (MSG) data sets were generated to characterize component population structure and infrapopulation diversity for a representative of each trypanorhynch suborder: the ray-hosted Rhinoptericola megacantha (Trypanobatoida) and the shark-hosted Callitetrarhynchus gracilis (Trypanoselachoida). Adults of R. megacantha are more host-specific and less broadly distributed than adults of C. gracilis, allowing correlation between these factors and genetic structure. Replicate tapeworm specimens were sequenced from the same host individual, from multiple conspecific hosts within and across geographic regions, and from multiple definitive host species. For R. megacantha, population structure coincided with geography rather than host species. For C. gracilis, limited population structure was found, suggesting a potential link between degree of host specificity and structure. Conspecific trypanorhynchs from the same host individual were found to be as, or more, genetically divergent from one another as from conspecifics from different host individuals. For both species, high levels of homozygosity and positive FIS values were documented.

Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes.

The enormous population sizes and wide biogeographical distribution of many microbial eukaryotes set the expectation of high levels of intraspecific genetic variation. However, studies investigating protist populations remain scarce, mostly due to limited 'omics data. Instead, most genetics studies of microeukaryotes have thus far relied on single loci, which can be misleading and do not easily allow for detection of recombination, a hallmark of sexual reproduction. Here, we analyze >40 genes from 72 single-cell transcriptomes from two morphospecies - Hyalosphenia papilio and Hyalosphenia elegans - of testate amoebae (Arcellinida, Amoebozoa) to assess genetic diversity in samples collected over four years from New England bogs. We confirm the existence of cryptic species based on our multi-locus dataset, which provides evidence of recombination within and high levels of divergence between the cryptic species. At the same time, total levels of genetic diversity within cryptic species are low, suggesting that these abundant organisms have small effective population sizes, perhaps due to extinction and repopulation events coupled with efficient modes of dispersal. This study is one of the first to investigate population genetics in uncultivable heterotrophic protists using transcriptomics data and contributes towards understanding cryptic species of non-model microeukaryotes.

Genetic population structure of the precious coral Corallium japonicum in the Northwest Pacific

Population sizes of the Japanese red coral Corallium japonicum have been severely affected by poaching and overfishing. Although genetic structure and connectivity patterns are considered important parameters for conservation strategies, there are few studies focusing on the population genetics of C. japonicum in the Northwest Pacific. We examined the genetic population structure of C. japonicum, in the Northwest Pacific. We used restriction-site-associated DNA sequencing (RAD-seq), which can be used to identify genome-wide single-nucleotide polymorphism (SNPs), to reveal detailed within-species genetic variations. Using the variable SNP loci identified from this analysis, we successfully evaluated the population-level genetic diversity and patterns of gene flow among multiple populations of C. japonicum around Japan. The results of genetic analysis basically showed that gene flow is widely maintained in the geographic range examined in this study, but the analysis in combination with larval dispersal simulations revealed several populations that were genetically distinct from the other populations, suggesting geographically limited gene flows. The information obtained from this study will be useful for the design of effective management schemes for C. japonicum, which is under threat from overfishing.

Combined empirical techniques reveal key role for variation in plasticity in a novel environment.

This article is a Commentary on Walter et al. (2023), 239: 374–387.

The Origin and Invasion Pathway of Brown Rats Rattus norvegicus on Dok-Do Island Revealed by Genome-Wide Markers from 3-RADseq Approach

Biological invasions are known to cause local extinctions on islands. Dok-do, a small, remote volcanic island in the East Sea of Korea in the western Pacific, has recently been invaded by rats, posing ecological problems. To infer their origin and invasion pathway, we collected rats from Dok-do and from the potential introduction source locations, Ulleung-do in the Pacific Ocean, and four east coastal ports. First, we identified that the brown rat (Rattus norvegicus) was the only rat species occurring at collecting sites based on the key morphological characteristics. To determine the population-level genetic diversity pattern, we applied the 3-RADseq approach. After a series of filtrations (minor allele frequency < 0.05, Hardy-Weinberg equilibrium p < 1 × 10-7), 4042 SNPs were retained for the final dataset from the 25,439 SNPs initially isolated. The spatial structure and genetic diversity pattern of brown rats suggested that the rat population on Dok-do was likely introduced from Ulleung-do. Our work provides practical information that will assist in the management of invasive brown rats in vulnerable island ecosystems.

Protein coding variation in the J:ARC and J:DO outbred laboratory mouse stocks provides a molecular basis for distinct research applications.

Outbred laboratory mice (Mus musculus) are readily available and have high fecundity, making them a popular choice in biomedical research, especially toxicological and pharmacological applications. Direct high throughput genome sequencing (HTS) of these widely used research animals is an important genetic quality control measure that enhances research reproducibility. HTS data have been used to confirm the common origin of outbred stocks and to molecularly define distinct outbred populations. But these data have also revealed unexpected population structure and homozygosity in some populations; genetic features that emerge when outbred stocks are not properly maintained. We used exome sequencing to discover and interrogate protein-coding variation in a newly established population of Swiss-derived outbred stock (J:ARC) that is closely related to other, commonly used CD-1 outbred populations. We used these data to describe the genetic architecture of the J:ARC population including heterozygosity, minor allele frequency, LD decay, and we defined novel, protein-coding sequence variation. These data reveal the expected genetic architecture for a properly maintained outbred stock and provide a basis for the on-going genetic quality control. We also compared these data to protein-coding variation found in a multiparent outbred stock, the Diversity Outbred (J:DO). We found that the more recently derived, multiparent outbred stock has significantly higher interindividual variability, greater overall genetic variation, higher heterozygosity, and fewer novel variants than the Swiss-derived J:ARC stock. However, among the novel variants found in the J:DO stock, significantly more are predicted to be protein-damaging. The fact that individuals from this population can tolerate a higher load of potentially damaging variants highlights the buffering effects of allelic diversity and the differing selective pressures in these stocks. While both outbred stocks offer significant individual heterozygosity, our data provide a molecular basis for their intended applications, where the J:DO are best suited for studies requiring maximum, population-level genetic diversity and power for mapping, while the J:ARC are best suited as a general-purpose outbred stock with robust fecundity, relatively low allelic diversity, and less potential for extreme phenotypic variability.

Integrative Taxonomy Reveals a Panmictic Population of Henneguya longisporoplasma n. sp. (Cnidaria: Myxozoa) in the Amazon Basin.

Henneguya Thélohan, 1892 is one of the most species-rich genera of myxosporean parasites and infects fish around the world. The present study describes a new species infecting the gill filaments, fins, and kidneys of Plagioscion squamosissimus (Heckel, 1840), an economically important freshwater fish distributed in watersheds in the north of South America. A total of 108 P. squamosissimus specimens were examined from three geographic localities in the Amazon basin: the Lago Grande do Curuai, a marginal lake of the Amazon River; the Tapajós River, in the state of Pará; and the Solimões River, in the state of Amazonas, Brazil. The analyses were based on the myxospore morphology, ribosomal DNA sequencing, phylogeny, prevalence, and geographic distribution of the host and its parasite. Parasite prevalences were 50% in both the Tapajós and Solimões rivers, and 35.4% in the Lago Grande do Curuai. In terms of the site of infection, the prevalence total was 23.1% in the gill filament, 29.6% in the fins, and 1.8% in the kidney. Regarding gender, the prevalence was 59.5% for males, 32.5% for females, and 21.7% for undetermined sex. The specimens found here were both morphologically and molecularly identical regardless of the infected organ and geographic locality, but distinct from all other Henneguya species, revealing that the parasite reported represents a novel species named Henneguya longisporoplasma n. sp. Despite the sampling being carried out in three different geographic localities of the Amazon basin, no population-level genetic variation was observed, even in the typically more variable ITS-1 region, revealing a panmictic population of H. longisporoplasma n. sp. in this large watershed. Maximum likelihood and Bayesian analyses showed the novel Henneguya clustered as a sister branch of the subclade formed of Henneguya that infect fish belonging to the family Cichlidae. A novel Henneguya species was identified parasitizing P. squamosissimus. The parasite presented wide geographic distribution in the Amazon basin and genetic analyses showed it as revealing a panmictic population.

Evidence of selection in the uncoupling protein 1 gene region suggests local adaptation to solar irradiance in savannah monkeys (Chlorocebus spp.).

In the last 300 thousand years, the genus Chlorocebus expanded from equatorial Africa into the southernmost latitudes of the continent, where colder climate was a probable driver of natural selection. We investigated population-level genetic variation in the mitochondrial uncoupling protein 1 (UCP1) gene region-implicated in non-shivering thermogenesis (NST)-in 73 wild savannah monkeys from three taxa representing this southern expansion (Chlorocebus pygerythrus hilgerti, Chlorocebus cynosuros and Chlorocebus pygerythrus pygerythrus) ranging from Kenya to South Africa. We found 17 single nucleotide polymorphisms with extended haplotype homozygosity consistent with positive selective sweeps, 10 of which show no significant linkage disequilibrium with each other. Phylogenetic generalized least-squares modelling with ecological covariates suggest that most derived allele frequencies are significantly associated with solar irradiance and winter precipitation, rather than overall low temperatures. This selection and association with irradiance is demonstrated by a relatively isolated population in the southern coastal belt of South Africa. We suggest that sunbathing behaviours common to savannah monkeys, in combination with the strength of solar irradiance, may mediate adaptations to thermal stress via NST among savannah monkeys. The variants we discovered all lie in non-coding regions, some with previously documented regulatory functions, calling for further validation and research.

Inbreeding depression and the probability of racing in the Thoroughbred horse.

Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs of homozygosity (ROH) using 297 K SNP genotypes from 6128 horses born in Europe and Australia, of which 13.2% were unraced. We show that a 10% increase in inbreeding (FROH) is associated with a 7% lower probability of ever racing. Moreover, a ROH-based genome-wide association study identified a haplotype on ECA14 which, in its homozygous state, is linked to a 32.1% lower predicted probability of ever racing, independent of FROH. The haplotype overlaps a candidate gene, EFNA5, that is highly expressed in cartilage tissue, which when damaged is one of the most common causes of catastrophic musculoskeletal injury in racehorses. Genomics-informed breeding aiming to reduce inbreeding depression and avoid damaging haplotype carrier matings will improve population health and racehorse welfare.

Spatial Variation of Acanthophlebia cruentata (Ephemeroptera), a Mayfly Endemic to Te Ika-a-Māui-North Island of Aotearoa, New Zealand.

Simple SummaryPatterns of variation within a widespread species can provide evidence of population history. Adjacent stable populations with gene flow show clinal genetic divergence forming a pattern of isolation by distance. Populations that have grown due to an increase in potential habitat such as forest cover since the last glacial maximum will have low genetic variation showing patterns of range expansion. The mayfly Acanthophlebia cruentata of Aotearoa, New Zealand, is widespread in streams of North Island but absent from the cooler South Island. Mayfly nymphs are restricted to streams but adults fly, facilitating gene flow among catchments. We detected higher genetic diversity at lower latitudes of this mayfly’s range compared to most of its distribution, concordant with predictions of limited forest cover in New Zealand during Pleistocene glacial periods. A signature of recent range expansion was observed in the higher latitudes. Despite initial observation suggesting mayfly size correlated with latitude, we found sex, elevation and sampling date were significant predictors of size, and some size variation is also explained by three regional groups based on haplotype distribution.The mayfly Acanthophlebia cruentata of Aotearoa, New Zealand, is widespread in Te Ika-a-Māui North Island streams, but has never been collected from South Island despite land connection during the last glacial maximum. Population structure of this mayfly might reflect re-colonisation after volcanic eruptions in North Island c1800 years ago, climate cycling or conceal older, cryptic diversity. We collected population samples from 33 locations to estimate levels of population genetic diversity and to document phenotypic variation. Relatively low intraspecific haplotype divergence was recorded among mitochondrial cytb sequences from 492 individuals, but these resolved three geographic-haplotype regions (north, west, east). We detected a signature of isolation by distance at low latitudes (north) but evidence of recent population growth in the west and east. We did not detect an effect of volcanic eruptions but infer range expansion into higher latitudes from a common ancestor during the last glacial period. As judged from wing length, both sexes of adult mayflies were larger at higher elevation and we found that haplotype region was also a significant predictor of Acanthophlebia cruentata size. This suggests that our mitochondrial marker is concordant with nuclear genetic differences that might be explained by founder effect during range expansion.

Differentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations.

ABSTRACTSome marine microbes are seemingly “ubiquitous,” thriving across a wide range of environmental conditions. While the increased depth in metagenomic sequencing has led to a growing body of research on within-population heterogeneity in environmental microbial populations, there have been fewer systematic comparisons and characterizations of population-level genetic diversity over broader expanses of time and space. Here, we investigated the factors that govern the diversification of ubiquitous microbial taxa found within and between ocean basins. Specifically, we use mapped metagenomic paired reads to examine the genetic diversity of ammonia-oxidizing archaeal (“Candidatus Nitrosopelagicus brevis”) populations in the Pacific (Hawaii Ocean Time-series [HOT]) and Atlantic (Bermuda Atlantic Time Series [BATS]) Oceans sampled over 2 years. We observed higher nucleotide diversity in “Ca. N. brevis” at HOT, driven by a higher rate of homologous recombination. In contrast, “Ca. N. brevis” at BATS featured a more open pangenome with a larger set of genes that were specific to BATS, suggesting a history of dynamic gene gain and loss events. Furthermore, we identified highly differentiated genes that were regulatory in function, some of which exhibited evidence of recent selective sweeps. These findings indicate that different modes of genetic diversification likely incur specific adaptive advantages depending on the selective pressures that they are under. Within-population diversity generated by the environment-specific strategies of genetic diversification is likely key to the ecological success of “Ca. N. brevis.”IMPORTANCE Ammonia-oxidizing archaea (AOA) are one of the most abundant chemolithoautotrophic microbes in the marine water column and are major contributors to global carbon and nitrogen cycling. Despite their ecological importance and geographical pervasiveness, there have been limited systematic comparisons and characterizations of their population-level genetic diversity over time and space. Here, we use metagenomic time series from two ocean observatories to address the fundamental questions of how abiotic and biotic factors shape the population-level genetic diversity and how natural microbial populations adapt across diverse habitats. We show that the marine AOA “Candidatus Nitrosopelagicus brevis” in different ocean basins exhibits distinct modes of genetic diversification in response to their selective regimes shaped by nutrient availability and patterns of environmental fluctuations. Our findings specific to “Ca. N. brevis” have broader implications, particularly in understanding the population-level responses to the changing climate and predicting its impact on biogeochemical cycles.

Genetic Diversity on a Rare Terrestrial Orchid, Habenaria linearifolia in South Korea: Implications for Conservation Offered by Genome-Wide Single Nucleotide Polymorphisms.

Monitoring intraspecific diversity offers invaluable insights on conservation practices as the variation is the product of species evolution. Accordingly, the role of population genetic diversity has drawn great attention over the last century responding to the biodiversity loss induced by a series of anthropogenic changes. Orchids are one of the most diverse, yet ironically most rapidly disappearing plant groups due to the specialized habitat preferences. Thus, population-level genetic diversity studies may offer a powerful tool for orchid conservation programs. Using the 3 restriction site-associated DNA (3RAD) approach, 2,734 genome-wide single nucleotide polymorphisms (SNPs) were isolated. With the 2,734 SNPs, we investigated genetic diversity and population structure on 72 individuals of Habenaria linearifolia and Habenaria cruciformis in South Korea. Overall, the genetic diversity was well maintained in South Korean Habenaria, but high FST values were estimated suggesting large population diversification with limited gene flow. Bayesian assignment analysis revealed a morphologically cryptic diversity pattern in Jeju Island populations, which might serve as an evolutionarily significant unit.

Phylogeography of the Neotropical sciurid Guerlinguetus brasiliensis (Rodentia: Sciuridae)

Abstract The Brazilian squirrel Guerlinguetus brasiliensis is the only sciurid species occurring in the Atlantic Forest. We investigated the geographical distribution of the genetic diversity of this sciurid species across the Central Corridor of the Atlantic Forest, using two mitochondrial markers and one nuclear marker. We also inferred the demographic history and estimated the present and past habitat suitability for the species. We found strong mitochondrial DNA structure, possibly with both the Doce River and the valley of Paraíba do Sul River restricting gene flow between populations. The demography and ecological niche modelling highlighted a shared evolutionary history amongst several forest-dependent species in the Atlantic Forest. A pattern of isolation by distance was also found, revealing the low mobility and/or dispersal capacity of the species. Further data are required to disentangle exactly how past and/or recent habitat changes have affected population-level genetic diversity of G. brasiliensis.

The impact of urbanization on outcrossing rate and population genetic variation in the native wildflower, Impatiens capensis

Abstract Cities are one of the fastest growing ecosystems on the planet, and conserving urban biodiversity is of primary importance. Urbanization increases habitat fragmentation and may be particularly problematic for native plant species which often exist in small, remnant populations in cities. We studied the effects of urbanization on Impatiens capensis, a self-compatible native wildflower, which is an important nectar and pollen source for native bees and hummingbirds. We sampled I. capensis from six populations located in urban and rural habitats in Toronto, Ontario, Canada. We sequenced the DNA of 43 families (N = 86 individuals) using genotype-by-sequencing to obtain 5627 single nucleotide polymorphisms. From each parent and offspring, we estimated individual outcrossing rates, population-level genetic diversity and genetic structure among populations. We found that 95% of plants were outcrossed, and populations were genetically differentiated, where urban populations contained a subset of the genetic variation found in rural populations. Urban populations exhibited lower genetic diversity than rural populations, and we detected a relationship between population census size and habitat on genetic diversity. Despite high outcrossing rates, our results suggest that urbanization reduces the genetic diversity of I. capensis populations, potentially increasing the vulnerability of these populations to long-term population declines and extirpation in response to urbanization.

The role of genome duplication in big sagebrush growth and fecundity.

Adaptive traits can be dramatically altered by genome duplication. The study of interactions among traits, ploidy, and the environment are necessary to develop an understanding of how polyploidy affects niche differentiation and to develop restoration strategies for resilient native ecosystems. Growth and fecundity were measured in common gardens for 39 populations of big sagebrush (Artemisia tridentata) containing two subspecies and two ploidy levels. General linear mixed-effect models assessed how much of the trait variation could be attributed to genetics (i.e., ploidy and climatic adaptation), environment, and gene-environment interactions. Growth and fecundity variation were explained well by the mixed models (80% and 91%, respectively). Much of the trait variation was attributed to environment, and 15% of variation in growth and 34% of variation in seed yield were attributed to genetics. Genetic trait variation was mostly attributable to ploidy, with much higher growth and seed production in diploids, even in a warm-dry environment typically dominated by tetraploids. Population-level genetic variation was also evident and was related to the climate of each population's origin. Ploidy is a strong predictor growth and seed yield, regardless of common-garden environment. The superior growth and fecundity of diploids across environments raises the question as to how tetraploids can be more prevalent than diploids, especially in warm-dry environments. Two hypotheses that may explain the abundance of tetraploids on the landscape include selection for drought resistance at the seedling stage, and greater competitive ability in water uptake in the upper soil horizon.

High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing.

Simple SummaryDomestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Development of mitochondrial markers has allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Reduction in the genetic diversity of livestock also decreases the species resilience and adaptability to local environmental conditions and disease outbreaks, thus leading us to hypothesize that Thai dairy cattle populations are approaching a status of low genetic variability. In the present study, the genetic diversity and structure of Thai dairy cattle populations were investigated, both within and between populations, for 179 individuals from nine provinces of Thailand. Mitochondrial D-loop sequence data were collected and analyzed. To minimize the degree of relationship among individuals, cattle were randomly selected based on details interviewed with the owners. The results will facilitate an improved understanding of the fundamental elements involved in breeding strategies and promote sustainable livestock utilization.Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup “I”, were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.

Colonizations cause diversification of host preferences: A mechanism explaining increased generalization at range boundaries expanding under climate change.

As species' poleward range limits expand under climate change, generalists are expected to be better colonists than specialists, extending their ranges faster. This effect of specialization on range shifts has been shown, but so has the reverse cause-effect: in a global meta-analysis of butterfly diets, it was range expansions themselves that caused increases in population-level diet breadth. What could drive this unexpected process? We provide a novel behavioral mechanism by showing that, in a butterfly with extensive ecotypic variation, Edith's checkerspot, diet breadths increased after colonization events as diversification of individual host preferences pulled novel hosts into population diets. Subsequently, populations that persisted reverted toward monophagy. We draw together three lines of evidence from long-term studies of 15 independently evolving populations. First, direct observations showed a significant increase in specialization across decades: in recent censuses, eight populations used fewer host genera than in the 1980s while none used more. Second, behavioral preference-testing experiments showed that extinctions and recolonizations at two sites were followed, at first by diversification of heritable preference ranks and increases in diet breadth, and subsequently by homogenization of preferences and contractions of diet breadth. Third, we found a significant negative association in the 1980s between population-level diet breadth and genetic diversity. Populations with fewer mtDNA haplotypes had broader diets, extending to 3-4 host genera, while those with higher haplotype diversity were more specialized. We infer that diet breadth had increased in younger, recently colonized populations. Preference diversification after colonization events, whether caused by (cryptic) host shifts or by release of cryptic genetic variation after population bottlenecks, provides a mechanism for known effects of range shifts on diet specialization. Our results explain how colonizations at expanding range margins have increased population-level diet breadths, and predict that increasing specialization should accompany population persistence as current range edges become range interiors.

A population genetics study of three native Mexican woody bamboo species of Guadua (Poaceae: Bambusoideae: Bambuseae: Guaduinae) using nuclear microsatellite markers

Background: Sporadic flowering contributes significantly to genetic diversity and connectivity among populations. Woody bamboos present sporadic or gregarious flowering patterns with long flowering cycles. In this study, we analyze the genetic diversity of three Guadua species distributed along the Gulf of Mexico slope that have different patterns of flowering. &#x0D; Questions: (1) Are the three Guadua species genetically differentiated? (2) Does the vulnerable species G. inermis have low levels of genetic diversity? (3) What is the relative contribution of geographic and environmental factors to the genetic structure of G. inermis ?&#x0D; Species studied: Guadua inermis , G. amplexifolia and G. tuxtlensis &#x0D; Study site and dates: During 2014 and 2015, we collected samples of G. inermis in Puebla and southeastern Mexico, G. amplexifolia in Veracruz and Oaxaca, and G. tuxtlensis in southern Veracruz.&#x0D; Methods: We successfully amplified five of nine SSR markers, and genotyped a total of 155 samples.&#x0D; Results: The three Guadua species were genetically differentiated. For G. inermis , we found high levels of population genetic diversity, which are relatively higher than those of other monocot species. Genetic differentiation was high and three groups were detected: north, central and south. We found a significant association between genetic distances and the maximum temperature of the warmest month, but not with geographic distance. &#x0D; Conclusions: Our study is the first to analyze levels of genetic diversity in Mexican bamboos and confirms their taxonomic identity. G. inermis has a strong genetic structure, even when populations are geographically close.