A genetic history of the pre-contact Caribbean.

The influence of genetic drift on the formation and stability of polymorphisms arising from negative frequency-dependent selection

A fundamental challenge in population genetics is to understand the role of ecological and historical processes in shaping genetic diversity patterns within and among species. Based on a set of nuclear microsatellite loci, we conducted a comparative study of the genetic diversity and structure of two epiphytic plant species: Vriesea simplex and V. scalaris (Bromeliaceae), endemic to the Brazilian Atlantic Rainforest. The results showed contrasting genetic diversity and structure patterns according to variation in reproductive systems of these species. High genetic diversity, high effective population sizes and low genetic differentiation were observed in the mainly outcrossing V. simplex populations. In contrast, low genetic diversity, low effective population sizes and high genetic differentiation were detected in the mainly selfing V. scalaris populations. Accordingly, the isolation-by-distance indicated stronger population structures in V. scalaris than in V. simplex. Both species showed a similar phylogeographic north-south split across the Atlantic Rainforest, suggesting possible multiple refugia in this biome. Historical climatic changes during the Pleistocene were possible determinants of the genetic diversity and structure of these species in the Atlantic Rainforest. Divergent mating systems (selfing vs. outcrossing), genetic drift and colonization history influenced the genetic diversity and structure of these Neotropical plant species.

A modified Wright–Fisher model that incorporates Ne: A variant of the standard model with increased biological realism and reduced computational complexity

Migratory birds generally have higher dispersal propensity than resident species and are thus expected to show less genetic differentiation. On the other hand, specific migration patterns may promote genetic structure, such as in situations where migratory divides impede random mixing of individuals. Here we investigated population genetic structure and gene flow patterns in a polytypic passerine, the reed warbler Acrocephalus scirpaceus which shows a migratory divide in central Europe. Using ten polymorphic microsatellite loci and extensive sampling we found low but significant overall genetic differentiation (FST0.013, G’ST0.078, D0.063). Hierarchical F-statistics and barrier analyses showed low but significant genetic differentiation of Iberian populations, and also slight genetic differences across the migratory divide and between subspecies ( A. s. scirpaceus and A. s. fuscus). Three individual-based Bayesian methods, however, inferred a single genetic unit. Our study thus found low levels of genetic differentiation among reed warbler populations but this genetic differentiation was not pronounced enough to detect a clear population structure using the microsatellite data and no prior information on geographic location of the sampled individuals. This result indicates high levels of gene flow and suggests a possibly recent divergence of European populations after a rapid range expansion. Further studies are necessary to assess divergence times and to reveal the evolutionary history of the reed warbler populations.

Background and aims – The study of factors and processes involved in evolutionary divergence can inform how biodiversity is generated and maintained. We evaluate shifts in phenology or in pollination systems as potential barriers to gene exchange and thus promoters of divergence at the population-species boundary in the plant ring-species Euphorbia tithymaloides in the Caribbean. Material and methods – Combining collections-based and field-based observations and measurements, we evaluate evidence supporting that shifts in tempo of reproductive activity (floral phenology) or pollinator guilds (using visitation as a proxy) could be acting as mechanisms promoting divergence in E. tithymaloides. We focus on the geographic region where evolutionary divergence in this species has been documented: Greater and Lesser Antilles. Phenology data were derived from herbaria and online databases, for a total of 376 records across the Greater and Lesser Antilles. We quantified and characterized reward (nectar n = 13 sites) and gathered visitation data using direct observation (n = 12 sites) for a total of over 133 hours of observation/site. Key results – The peak of floral activity of E. tithymaloides is in winter, when days are short (~late October–late May). Under natural conditions, plants in the Antilles produce up to 22.4 µL of nectar, with mean sugar concentrations of ~ 46.5 ºBrix that amount to up to 10.3 mg of total sugars, with no significant differences observed between plants of the Lesser and Greater Antilles. Hummingbirds are the main floral visitors of E. tithymaloides in both areas: Greater Antilles: 61%, Lesser Antilles: 85%, and network analyses support a floral visitor community turnover across islands/countries. Conclusion – Evolutionary divergence in Caribbean E. tithymaloides along the Greater and Lesser Antilles is not accompanied by shifts in floral phenology or pollinator systems. Other factors, like pollinator turnover or pollinator-plant trait matching, might be at play. We outline hypotheses to this effect.

Heavy fishing and other anthropogenic influences can have profound impact on a species' resilience to harvesting. Besides the decrease in the census and effective population size, strong declines in mature adults and recruiting individuals may lead to almost irreversible genetic changes in life-history traits. Here, we investigated the evolution of genetic diversity and effective population size in the heavily exploited sole (Solea solea), through the analysis of historical DNA from a collection of 1379 sole otoliths dating back from 1957. Despite documented shifts in life-history traits, neutral genetic diversity inferred from 11 microsatellite markers showed a remarkable stability over a period of 50 years of heavy fishing. Using simulations and corrections for fisheries induced demographic variation, both single-sample estimates and temporal estimates of effective population size (N(e) ) were always higher than 1000, suggesting that despite the severe census size decrease over a 50-year period of harvesting, genetic drift is probably not strong enough to significantly decrease the neutral diversity of this species in the North Sea. However, the inferred ratio of effective population size to the census size (N(e) /N(c) ) appears very small (10(-5) ), suggesting that overall only a low proportion of adults contribute to the next generation. The high N(e) level together with the low N(e) /N(c) ratio is probably caused by a combination of an equalized reproductive output of younger cohorts, a decrease in generation time and a large variance in reproductive success typical for marine species. Because strong evolutionary changes in age and size at first maturation have been observed for sole, changes in adaptive genetic variation should be further monitored to detect the evolutionary consequences of human-induced selection.

Primarily a taxonomic review of the West Indian elements of the selenophorine Harpalini, this paper includes a classification, a key, descriptions and illustrations of taxa, re-rankings, and new synonymies. In total, 45 species and subspecies are treated, six of which are described as new. A new genus and new species are as follows, with type localities in parentheses: Paraulacoryssus gen. n., (type species Selenophorus puertoricensis Mutchler, 1934); Neodiachipteryx davidsoni sp. n., (Zamba, Dominican Republic); Selenophorus spinosus sp. n., seriatoporus species group (Benjamin Constant, state of Amazonas, Brazil); Selenophorus obtusoides sp. n., parumpunctatus species group (near Soroa, Pinar del Rio Province, Cuba); Selenophorus iviei sp. n., nonseriatus species group (Big River, Montserrat, 16°45.719N', 62°11.335W'); Selenophorus irec sp. n., nonseriatus species group (Vernou, Guadeloupe, Lesser Antilles); and Selenophorus fabricii sp. n., opalinus species group (Cabo Rojo, Pedernales Province, Dominican Republic). This last species was misidentified as Selenophorus integer (Fabricius). In turn, that species was misidentified as Selenophorus chalybeus Dejean. Selenophorus chalybeus Dejean is a junior synonym of Selenophorus integer Fabricius, syn. n.; and Isopleurus macleayi Kirby is a junior synonym of Selenophorus pyritosus Dejean, syn. n.Biogeographically, log of land area plotted against log of number of species shows that the equilibrium theory of biogeography applies to the West Indian selenophorine fauna.Taxonomically, the selenophorine taxa of the West Indies are arranged in eight genera. The 30 species/subspecies of Selenophorus (sensu stricto) are arranged in 10 species groups. Geographically, the major sources of the selenophorines are the Bahamas, the Greater Antilles and Lesser Antilles. The West Indian islands probably have been invaded by 26 taxa. Of the currently extant taxa, 11 are classified as immigrant, meaning that they are represented both in the islands and on the mainland (South America or Middle America and southern Florida). Thirty three taxa are classified as precinctive, meaning that they originated where they are now living, the implication being that they have descended from immigrants, thus older in the islands than the current-day immigrants.It is postulated that the West Indian taxa represent three age groups: oldest, ancestors having reached the proto-Antilles by a landspan known as GAARlandia; a middle-age group (Neogene period), their ancestors having reached the islands by dispersal over water, between islands; and a young group of extant taxa, no older than the Pleistocene, also having reached the islands over water.

— We review historical and recent information on the distribution, status, and habitat associations of the West Indian manatee, Trichechus manatus, summarize threats to its continued survival, and discuss some biogeographical patterns of trichechids. Historical accounts indicate that manatees were once more common and that hunting has been responsible for declining numbers throughout much of their range. Small numbers occur throughout the Greater Antilles, where opportunistic taking by fishermen is a major source of mortality. Populations in Haiti, the Dominican Republic, and Jamaica are particularly vulnerable. Manatees have not been documented to occur in the Lesser Antilles since the 18th century, except for rare sightings in the Virgin Islands. Manatee sightings in the Bahamas are also rare; however, a recent dispersal from the northwest coast of Florida to the Bahamas has been documented. Manatees are relatively abundant in Belize compared with other countries of Central America. They persist in some of the large river systems of South America: the Rio Magdalena in Colombia, Rio Orinoco in Venezuela, and probably the Rio Mearim in Brazil. They are absent or scarce along most of the South American coast, except in the extensive coastal wetlands of Guyana and Suriname. At present, there are only three regions in Mexico where manatees are still commonly found. Manatees are widely distributed on both coasts of Florida, and some venture westward along the Gulf coast and northward along the Atlantic coast of the southeastern United States, primarily during the warm season. Heated industrial effluents along both coasts have influenced manatee distribution and migratory patterns in the United States. Illegal killing continues to threaten the survival of manatees in many countries. Despite protective measures to regulate boating activity, collision with boats is still the major cause of human-related manatee mortality in Florida. Habitat alteration is a growing concern in all countries. Manatees in the Greater Antilles and Central and South America belong to the same subspecies, T. manatus manatus. However, results of recent genetic analysis indicate greater similarity between the Florida manatee, T. manatus latirostris, and manatees in the Dominican Republic and Puerto Rico, than between the latter and manatees in South America. The highest genetic diversity is found along the northern coast of South America, at the core of the species’ range; marginal populations (in Florida, Mexico, and Brazil) were each found to be monomorphic (only one haplotype apiece) although distinct from one another. Salinity, temperature, water depth, currents, shelter from wave action, and availability of vegetation are important determining factors of manatee distribution. The association of T. manatus with freshwater sources is a highly consistent pattern. Throughout most of their range, manatees appear to prefer rivers and estuaries to marine habitats. The Amazonian species, T. inunguis, may be restricted to the Amazon River because of intolerance of salinity. Cool winters and gaps in suitable habitat on the northern Gulf coast, and the Straits of Florida to the south, serve as geographical barriers that isolate the Florida subspecies. Manatees in northeastern Brazil, at the southern end of the species’ range, may also be geographically isolated. Unlike the Florida subspecies, they no longer inhabit the subtropical to temperate portion of their historical range.

Whether old-growth (OG) forests have higher genetic diversity and effective population size, consequently higher conservation value and climate adaptive potential than second-growth (SG) forests, remain an unresolved issue. We have tested the hypothesis that old-growth forest tree populations have higher genetic diversity, effective population size (NE), climate adaptive potential and conservation value and lower genetic differentiation than second-growth forest tree populations, employing a keystone and long-lived conifer, eastern white pine (EWP; Pinus strobus). Genetic diversity and population structure of old-growth and second-growth populations of eastern white pine (EWP) were examined using microsatellites of the nuclear and chloroplast genomes and single nucleotide polymorphisms (SNPs) in candidate nuclear genes putatively involved in adaptive responses to climate and underlying multilocus genetic architecture of local adaptation to climate in EWP. Old-growth and second-growth EWP populations had statistically similar genetic diversity, inbreeding coefficient and inter-population genetic differentiation based on nuclear microsatellites (nSSRs) and SNPs. However, old-growth populations had significantly higher chloroplast microsatellites (cpSSRs) haploid diversity than second-growth populations. Old-growth EWP populations had significantly higher coalescence-based historical long-term NE than second-growth EWP populations, but the linkage disequilibrium (LD)-based contemporary NE estimates were statistically similar between the old-growth and second-growth EWP populations. Analyses of population genetic structure and inter-population genetic relationships revealed some genetic constitution differences between the old-growth and second-growth EWP populations. Overall, our results suggest that old-growth and second-growth EWP populations have similar genetic resource conservation value. Because old-growth and second-growth EWP populations have similar levels of genetic diversity in genes putatively involved in adaptive responses to climate, old-growth, and second-growth populations may have similar adaptive potential under climate change. Our results could potentially be generalized across most of the boreal and temperate conifer forest trees. Our study contributes to address a long-standing issue, advances research field and knowledge about conservation and ecological and climate adaptation of forest trees.

The Caribbean Basin is contained roughly between latitudes 10 to 27°N and longitudes 57 to 87°W. The basin which derives its name from the word “Carib”, name of one of the ancestral Indian groups of the region, is an archipelago curving 4,000 km from Florida in the north to Venezuela in the south (Figure 1). The west side faces Central America. The northwest boundary is the Gulf of Mexico which is itself separated from the Caribbean Sea by a line running between the Yucatan channel and Florida Keys. To the east, the basin is separated from the Atlantic Ocean by an arc of islands starting with the Bahamas to the north and ending with Grenada and Trinidad-Tobago in the south. The main chain of islands is the Greater Antilles comprising Cuba, Hispaniola (the Dominican Republic and Haiti), Jamaica and Puerto Rico. The narrower chain is the Lesser Antilles, a collection of smaller islands stretching from the Virgin Islands in the north to Grenada in the south. The Lesser Antilles is further divided into windward islands which lie south of latitude 15° and leeward islands which lie north of the line. The islands of the Lesser Antilles and the eastern Caribbean are used synonymously in this chapter. The Caribbean and West Indies are also used interchangeably to refer to all the islands in both the Greater and Lesser Antilles. In other contexts, these two terms, Caribbean and West Indies, also include all countries of Central America as well as Venezuela, Surinam, Guyana and Colombia on the South American mainland and the islands that form its north coast.

This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments-based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.

Large scale harvesting and other anthropogenic activities have caused severe population declines in many commercially important fish populations, but accurate information about census and effective population size is often hard to come by. Available evidence suggests that in marine fishes, effective population size (N e) is often several orders of magnitude smaller than census size, such that intensively harvested populations may be particularly vulnerable to loss of genetic diversity. The European whitefish (Coregonus lavaretus) has a long history of heavy exploitation in the Baltic Sea, and the Finnish commercial catch of the species has been substantially reduced, despite high fishing effort. We investigated the temporal genetic stability of migratory whitefish populations from two Finnish rivers (Tornionjoki and Kiiminkijoki), sampled at least twice between 1981 and 2006, by assaying variability in 21 microsatellite loci. Our results suggest a small, albeit significant (F ST = 0.004; p = 0.008) and temporally stable, degree of differentiation between rivers. However, in contrast to earlier reports, heterochronous runs (ascending groups) from Tornionjoki did not exhibit significant genetic divergence. Bayesian estimates of N e suggest substantial declines from historic levels dating to ca 250 years. Yet despite a probable decrease in census population size over the study period, we detected no significant change in contemporary N e. Within group genetic diversity appeared largely unchanged over this time frame; however, we detected a trend towards decreased differentiation between spawning groups (rivers) since the 1980s. These results are discussed in light of stocking programs and conservation of genetic diversity of natural populations.

The life cycle of most marine species is characterized by high fecundity, dispersal during a planktonic larval phase and a sessile or sedentary adult phase with large census population size (Figure 1). Many articles on marine population genetics start by recalling these main characteristics and ensuing expectations, namely: high genetic diversity within population, low genetic differentiation between populations, high influx of effectively selected advantageous and deleterious mutations, and a high migration load opposing local adaptation. Most of the time, this reminder serves to better emphasize the paradox that observations deviate from these expectations, the most popular being genetic differentiation despite larval dispersal, challenging the idea that marine populations are open and well connected, just followed by pervasive local adaptation, challenging the idea that high migration rates prevent the establishment of locally adapted alleles in the sea, and finally low effective population size ( N e) despite large census size ( N ). The list of such counterexamples became so long that what was initially thought paradoxical finally became a shift to a new paradigm (Hauser and Carvalho 2008): (1) larval dispersal would be less effective than expected to homogenize allele frequencies between populations with high rates of self-recruitment, as, for example, in coral reef fishes (Palumbi and Warner 2003; Jones et al. 2005), (2) selection would be rampant in genomes and easy to identify with genome scans, as, for example, adaptation to brackish waters of the Baltic Sea that would target nothing less than ∼500 loci homogeneously distributed in the herring genome (Lamichhaney et al. 2012; Martinez Barrio et al. 2016), and (3) genetic drift would be stronger than thought owing to a very low proportion of individuals effectively contributing to the following generation, as, for example, in exploited fish and shellfish stocks (Hauser et al. 2002; Ovenden et al. …

Camellia oleifera is a subtropical evergreen plant. Cultivated C. oleifera is the most important woody oil crop in China. Wild C. oleifera is an essential genetic resource for breeding. The patterns of genetic differentiation among altitudes/latitudes in wild C. oleifera are still unknown. Camellia oleifera may be predominantly hexaploid. The characteristics of polyploidy may lead to considerable biases in estimates of genetic diversity and differentiation. Our study used C. oleifera as a case study for analysing genetic diversity, structure and differentiation in polyploid plants using simple sequence repeats (SSRs). Wild C. oleifera samples were collected at different altitudes on the Jinggang and Lu mountains of China. The ploidy levels were determined with flow cytometry analysis. Eight highly polymorphic SSRs were used to genotype the samples. Genetic diversity and structure were analysed. Various estimates of genetic differentiation were compared. The flow cytometry results indicated that wild C. oleifera samples were all hexaploid at various altitudes of the Jinggang and Lu mountains. High levels of genetic diversity were found on both the Jinggang and Lu mountains. Genetic structure analyses indicated clear genetic differentiation between the Jinggang and Lu mountains and lower genetic differentiation among altitudes within each mountain. Classical genetic differentiation estimates of Fst failed to discriminate genetic differentiation between and within mountains. The Rho statistic showed a moderate level of genetic differentiation between mountains and lower levels of genetic differentiation within each mountain. Our study demonstrates that Rho is the statistic of choice for estimating genetic differentiation in polyploids.

A primary objection from a population genetics perspective to a multiregional model of modern human origins is that the model posits a large census size, whereas genetic data suggest a small effective population size. The relationship between census size and effective size is complex, but arguments based on an island model of migration show that if the effective population size reflects the number of breeding individuals and the effects of population subdivision, then an effective population size of 10,000 is inconsistent with the census size of 500,000 to 1,000,000 that has been suggested by archeological evidence. However, these models have ignored the effects of population extinction and recolonization, which increase the expected variance among demes and reduce the inbreeding effective population size. Using models developed for population extinction and recolonization, we show that a large census size consistent with the multiregional model can be reconciled with an effective population size of 10,000, but genetic variation among demes must be high, reflecting low interdeme migration rates and a colonization process that involves a small number of colonists or kin-structured colonization. Ethnographic and archeological evidence is insufficient to determine whether such demographic conditions existed among Pleistocene human populations, and further work needs to be done. More realistic models that incorporate isolation by distance and heterogeneity in extinction rates and effective deme sizes also need to be developed. However, if true, a process of population extinction and recolonization has interesting implications for human demographic history.