The uneven phylogeny and biogeography of Erodium (Geraniaceae): radiations in the Mediterranean and recent recurrent intercontinental colonization

Background and Aims

The genus Erodium is a common feature of Mediterranean-type climates throughout the world, but the Mediterranean Basin has significantly higher diversity than other areas. The aim here is to reveal the biogeographical history of the genus and the causes behind the evolution of the uneven distribution.

Methods

Seventy-eight new nrITS sequences were incorporated with existing plastid data to explore the phylogenetic relationships and biogeography of Erodium using several reconstruction methods. Divergence times for major clades were calculated and contrasted with other previously published information. Furthermore, topological and temporal diversification rate shift analyses were employed using these data.

Key Results

Phylogenetic relationships among species are widely congruent with previous plastid reconstructions, which refute the classical taxonomical classification. Biogeographical reconstructions point to Asia as the ancestral area of Erodium, arising approx. 18 MYA. Four incidences of intercontinental dispersal from the Mediterranean Basin to similar climates are demonstrated. Increases in diversification were present in two independent Erodium lineages concurrently. Two bursts of diversification (3 MYA and 0·69 MYA) were detected only in the Mediterranean flora.

Conclusions

Two lineages diverged early in the evolution of the genus Erodium: (1) subgenus Erodium plus subgenus Barbata subsection Absinthioidea and (2) the remainder of subgenus Barbata. Dispersal across major water bodies, although uncommon, has had a major influence on the distribution of this genus and is likely to have played as significant role as in other, more easily dispersed, genera. Establishment of Mediterranean climates has facilitated the spread of the genus and been crucial in its diversification. Two, independent, rapid radiations in response to the onset of drought and glacial climate change indicate putative adaptive radiations in the genus.     

High intercontinental migration rates and population admixture in the sapstain fungus Ophiostoma ips

Ophiostoma ips is a common fungal associate of various conifer-infesting bark beetles in their native ranges and has been introduced into non-native pine plantations in the Southern Hemisphere. In this study, we used 10 microsatellite markers to investigate the population biology of O. ips in native (Cuba, France, Morocco and USA) and non-native (Australia, Chile and South Africa) areas to characterize host specificity, reproductive behaviour, and the potential origin as well as patterns of spread of the fungus and its insect vectors. The markers resolved a total of 41 alleles and 75 haplotypes. Higher genetic diversity was found in the native populations than in the introduced populations. Based on the origin of the insect vectors, the populations of O. ips in Australia would be expected to reflect a North American origin, and those in Chile and South Africa to reflect a European origin. However, most alleles observed in the native European population were also found in the native North American population; only the allele frequencies among the populations varied. This admixture made it impossible to confirm the origin of the introduced Southern Hemisphere (SH) populations of O. ips. There was also no evidence for specificity of the fungus to particular bark beetle vectors or hosts. Although O. ips is thought to be mainly self-fertilizing, evidence for recombination was found in the four native populations surveyed. The higher genetic diversity in the North American than in the European population suggests that North America could be the possible source region of O. ips.     

Temporal and spatial patterns of flight and body feather molt of Bank,Barn, and Cliff swallows in North and South America

Molt is energetically demanding and various molt strategies (i.e., molt series, duration, intensity, timing, and location) have evolved to reduce the negative fitness consequences of this process. As such, molt varies considerably among species. Identifying where and when specific feathers are molted is also crucial to inform species‐specific studies using stable isotope markers to assign individuals to geographical regions where they molt. Using museum specimens, we examined the molt of three species of migratory swallows in the Americas: Bank Swallows (Riparia riparia), Barn Swallows (Hirundo rustica), and Cliff Swallows (Petrochelidon pyrrhonota). All three species have one primary and two secondary molt series. Bank and Cliff swallows had one rectrix molt series, and Barn Swallows molted the outer rectrix (R6) separately from the inner five rectrices (R1‐5). All three species have a relatively long flight feather molt duration (i.e., 140–183 days) and low molt intensity. Barn Swallows initiated flight feather molt in the fall, about 2 months later than Bank and Cliff swallows. Barn Swallows likely delay molt because of constraints associated with double brooding. For all three species, molt started with the primaries and inner secondaries and was closely followed by the rectrices and, finally, the outer secondaries. For those that began and then interrupted molt either in breeding areas or during fall migration, the first feathers molted were predominantly S8 and P1. All three species underwent body molt throughout the year, but most individuals molted their body plumage in wintering areas. We recommend that the most appropriate feathers for stable isotope research examining migratory connectivity and habitat use are either R2‐R4 or S2‐S4.     

Brief communication: the Thule migration: rejecting population histories using computer simulation

Locked within our genetic code are the histories of our genes and the genes of our ancestors. Deciphering a population's history from genetic data often involves lengthy investigations of many loci for many individuals. We test hypothetical population histories of the Thule expansion using a new coalescent simulation method that uses little more than mitochondrial haplogroup data. This new methodology rejects a severe bottleneck at expansion and reveals the range of probable population histories on which to focus future research.     

Adaptive site selection rules and variation in group size of barn swallows: individual decisions predict population patterns

Variation in group size is ubiquitous among socially breeding organisms. An alternative to the traditional examination of average reproductive success in groups of different sizes is to examine individual decision making by determining the cues used for site selection. Once factors used for decision making are known, one can determine whether group-level patterns, such as group size variation, are emergent properties of individual-level decision rules. The advantage of this alternative approach is that it can explain the distribution of group sizes rather than just the occurrence of optimal group sizes. Using barn swallows, I tested, but did not support, the hypothesis that individuals settle at sites based on the previous success of conspecifics (i.e., performance-based conspecific attraction). Instead, I demonstrate that an adaptive site selection decision rule--to breed where it is possible to reuse previously constructed nests--predicts 83% of the variation in the number of breeding pairs at a site. Furthermore, experimental nest removals demonstrated that settlement decisions are also strongly influenced by site familiarity. I discuss the interaction of the cue-based site selection rule with the occurrence of site fidelity and how, more generally, a consideration of individual-level decision rules can improve our understanding of variation in many social behaviors.     

Ancient DNA perspectives on American colonization and population history

Ancient DNA (aDNA) analyses have proven to be important tools in understanding human population dispersals, settlement patterns, interactions between prehistoric populations, and the development of regional population histories. Here, we review the published results of sixty-three human populations from throughout the Americas and compare the levels of diversity and geographic patterns of variation in the ancient samples with contemporary genetic variation in the Americas in order to investigate the evolution of the Native American gene pool over time. Our analysis of mitochondrial haplogroup frequencies and prehistoric population genetic diversity presents a complex evolutionary picture. Although the broad genetic structure of American prehistoric populations appears to have been established relatively early, we nevertheless identify examples of genetic discontinuity over time in select regions. We discuss the implications this finding may have for our interpretation of the genetic evidence for the initial colonization of the Americas and its subsequent population history.     

Maternal effects mediated by maternal age: from life histories to population dynamics

1. Maternal effects describe how mothers influence offspring life histories. In many taxa, maternal effects arise by differential resource allocation to young, often identified by variation in propagule size, and which affects individual traits and population dynamics. 2. Using a laboratory model system, the soil mite Sancassania berlesei, we show that, controlling for egg size, older mothers lay eggs that hatch later, develop more slowly, and mature at larger body sizes. 3. Such differences in life histories lead to marked population dynamical effects lasting for multiple generations, as evidenced by an experiment initiated with similarly sized eggs that came from young or old mothers. Differences in maturation from the initial cohort led to differences in population structure and life history that propagated the initial differences over time. 4. Maternal-age effects, which are not related to gross provisioning of the egg and are therefore phenotypically cryptic, can have profound implications for population dynamics, especially if environmental variation can affect the age structure of the adult population.     

Plant colonization of a bare peat surface: population changes and spatial patterns

Abstract. Changes in size and spatial arrangement of plant populations established on an initially bare peat surface were described over a period of 5 yr by following plant individuals on a 1-cm grid in an area of 10 m x 25 m. The spatial pattern of populations and association between species was analyzed statistically. The study site was very slowly colonized by 14 perennial plant species. The early successional stage was dominated by Carex rostrata, with a clumped spatial distribution, and the homogeneously distributed Eriophorum vaginatum and Pinus sylvestris. Both the growth in size of populations and changes in their spatial distribution were interpreted as a result of species dispersal ability, tolerance to severity of the substrate and pattern of reproduction.     

Merino and Merino-derived sheep breeds: a genome-wide intercontinental study

Background

Merino and Merino-derived sheep breeds have been widely distributed across the world, both as purebred and admixed populations. They represent an economically and historically important genetic resource which over time has been used as the basis for the development of new breeds. In order to examine the genetic influence of Merino in the context of a global collection of domestic sheep breeds, we analyzed genotype data that were obtained with the OvineSNP50 BeadChip (Illumina) for 671 individuals from 37 populations, including a subset of breeds from the Sheep HapMap dataset.

Results

Based on a multi-dimensional scaling analysis, we highlighted four main clusters in this dataset, which corresponded to wild sheep, mouflon, primitive North European breeds and modern sheep (including Merino), respectively. The neighbor-network analysis further differentiated North-European and Mediterranean domestic breeds, with subclusters of Merino and Merino-derived breeds, other Spanish breeds and other Italian breeds. Model-based clustering, migration analysis and haplotype sharing indicated that genetic exchange occurred between archaic populations and also that a more recent Merino-mediated gene flow to several Merino-derived populations around the world took place. The close relationship between Spanish Merino and other Spanish breeds was consistent with an Iberian origin for the Merino breed, with possible earlier contributions from other Mediterranean stocks. The Merino populations from Australia, New Zealand and China were clearly separated from their European ancestors. We observed a genetic substructuring in the Spanish Merino population, which reflects recent herd management practices.

Conclusions

Our data suggest that intensive gene flow, founder effects and geographic isolation are the main factors that determined the genetic makeup of current Merino and Merino-derived breeds. To explain how the current Merino and Merino-derived breeds were obtained, we propose a scenario that includes several consecutive migrations of sheep populations that may serve as working hypotheses for subsequent studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0139-z) contains supplementary material, which is available to authorized users.     

Genomic structures and population histories of linguistically distinct tribal groups of India

There are various conflicting hypotheses regarding the origins of the tribal groups of India, who belong to three major language groups--Austro-Asiatic, Dravidian and Tibeto-Burman. To test some of the major hypotheses we designed a genetic study in which we sampled tribal populations belonging to all the three language groups. We used a set of autosomal DNA markers, mtDNA restriction-site polymorphisms (RSPs) and mtDNA hypervariable segment-1 (HVS-1) sequence polymorphisms in this study. Using the unlinked autosomal markers we found that there is a fair correspondence between linguistic and genomic affinities among the Indian tribal groups. We reconstructed mtDNA RSP haplotypes and found that there is extensive haplotype sharing among all tribal populations. However, there is very little sharing of mtDNA HVS-1 sequences across populations, and none across language groups. Haplogroup M is ubiquitous, and the subcluster U2i of haplogroup U occurs in a high frequency. Our analyses of haplogroup and HVS-1 sequence data provides evidence in support of the hypothesis that the Austro-Asiatic speakers are the most ancient inhabitants of India. Our data also support the earlier finding that some of the western Eurasian haplogroups found in India may have been present in India prior to the entry of Aryan speakers. However, we do not find compelling evidence to support the theory that haplogroup M was brought into India on an "out of Africa" wave of migration through a southern exit route from Ethiopia. On the contrary, our data raise the possibility that this haplogroup arose in India and was later carried to East Africa from India.     

Using phylochronology to reveal cryptic population histories: review and synthesis of 29 ancient DNA studies

The evolutionary history of a population involves changes in size, movements and selection pressures through time. Reconstruction of population history based on modern genetic data tends to be averaged over time or to be biased by generally reflecting only recent or extreme events, leaving many population historic processes undetected. Temporal genetic data present opportunities to reveal more complex population histories and provide important insights into what processes have influenced modern genetic diversity. Here we provide a synopsis of methods available for the analysis of ancient genetic data. We review 29 ancient DNA studies, summarizing the analytical methods and general conclusions for each study. Using the serial coalescent and a model-testing approach, we then re-analyse data from two species represented by these data sets in a common interpretive framework. Our analyses show that phylochronologic data can reveal more about population history than modern data alone, thus revealing 'cryptic' population processes, and enable us to determine whether simple or complex models best explain the data. Our re-analyses point to the need for novel methods that consider gene flow, multiple populations and population size in reconstruction of population history. We conclude that population genetic samples over large temporal and geographical scales, when analysed using more complex models and the serial coalescent, are critical to understand past population dynamics and provide important tools for reconstructing the evolutionary process.     

Wild cherries invading natural grasslands: unraveling colonization history from population structure and spatial patterns

Invasive success of many fleshy-fruited plants has been linked to opportunistic interactions with generalist frugivores. Prunus mahaleb is a small tree, producing large quantities of little, bright black, sugary drupes that are consumed by vertebrates. It is native to the Mediterranean region but has become invasive in several countries. This study was carried out at a nature reserve including remnant mountain grasslands of high conservation value in the southern Argentine Pampas. Our aim is to reconstruct the colonization history of invading populations proposing a generalized model to describe the invasion process: colonization events result in the establishment of a founder tree followed by a lag phase until it reaches massive seed production and enables an increase in local recruitment and plant density. To test this hypothesis, we analyzed population age structures and contrasted them with those predicted using a Leslie matrix growth model. We found that matrix model predictions fit well to actual age structures. Our results reveal the existence of an 8–18-year lag period between the establishment of the founder tree and local effective recruitment. The end of this lag coincides with an abrupt increase in individual fruit production that may have a strong effect on bird attraction and successful seed dispersal. This lag phase represents an opportunity for preventing further spread of P. mahaleb. Early detection and rapid eradication of new invasion focuses should be targeted as a principal aim of an effective control strategy.     

What individual life histories can (and cannot) tell about population dynamics

We present an overview of a long-term research programme that is aimed at revealing the relations between individual feeding, growth, reproduction and mortality in Daphnia pulex and the state and dynamics of the population. We analyse a physiologically structured population model, in which individual performance is described using an energy budget model that incorporates a food dependence. The model predictions are shown to be at odds with experimental observations on populations of Daphnia. We argue that these discrepancies are primarily due to insufficient knowledge about the precise size-scaling of the food ingestion rate, which plays a central role in the competitive interaction among individuals. To a lesser extent, the discrepancies arise because details about the energy budget of individual Daphnia are not sufficiently known for the food conditions prevailing in population experiments.     

Contrasting population genetic patterns and evolutionary histories among sympatric Sonoran Desert cactophilic Drosophila

We studied population genetic differentiation in the sympatric Sonoran Desert cactophilic flies Drosophila pachea, D. mettleri and D. nigrospiracula across their continental and peninsular ranges. These flies show marked differences in ecology and behaviour including dispersal distances and host cactus specialization. Examination of a fragment of the mitochondrial cytochrome oxidase subunit I gene (mtCOI) reveals that the Sea of Cortez has constituted an effective dispersal barrier for D. pachea, leading to significant genetic differentiation between the continental and peninsular ranges of this species. No genetic differentiation was detected, however, within its continental and peninsular ranges. In contrast, our mtCOI-based results for D. mettleri and D. nigrospiracula are consistent with a previous allozyme-based study that showed no significant genetic differentiation between continental and peninsular ranges of these two species. For D. mettleri, we also found that the insular population from Santa Catalina Island, California, is genetically differentiated with respect to continental and peninsular localities. We discuss how differences in the genetic structure patterns of D. pachea, D. mettleri and D. nigrospiracula may correspond to differences in their dispersal abilities, host preferences and behaviour.     

Broad wintering range and intercontinental migratory divide within a core population of the near‐threatened pallid harrier

Aim To identify the migration routes and wintering grounds of the core populations of the near‐threatened pallid harrier, Circus macrourus, and highlight conservation needs associated with these phases of the annual cycle. Location Breeding area: north‐central Kazakhstan; Wintering areas: Sahel belt (Burkina Faso to Ethiopia) and north‐west India. Methods We used ring recovery data from Kazakhstan and satellite tracking data from 2007 to 2008 on six adults breeding in north‐central Kazakhstan to determine migration routes and locate wintering areas. In addition, one first‐year male was tagged in winter 2007–2008 in India. Results Data evidenced an intercontinental migratory divide within the core pallid harrier population, with birds wintering in either Africa or India. The six individuals tagged in north‐central Kazakhstan followed a similar route (west of the Caspian Sea and Middle East) towards east Africa, before spreading along the Sahel belt to winter either in Sudan, Ethiopia, Niger or Burkina Faso. Spring migration followed a shorter, more direct route, with marked interindividual variation. The bird tagged in India spent the summer in central Kazakhstan. Half of the signal losses (either because of failure or bird mortality) occurred on the wintering areas and during migration. Main conclusions Our study shows that birds from one breeding area may winter over a strikingly broad range within and across continents. The intercontinental migratory divide of pallid harriers suggests the coexistence of distinct migratory strategies within the core breeding population, a characteristic most likely shared by a number of threatened species in central Asia. Conservation strategies for species like the pallid harrier, therefore, require considering very large spatial scales with possibly area‐specific conservation issues. We highlight urgent research priorities to effectively inform the conservation of these species.     

Origins,ages and population histories: comparative phylogeography of endemic Hawaiian butterflyfishes (genus Chaetodon)

Aim To investigate phylogeographic relationships, genetic connectivity and potential colonization routes for Hawaii’s endemic butterflyfishes (family Chaetodontidae). Location The Hawaiian Archipelago (central Pacific Ocean). Methods Molecular genetic analysis of mitochondrial DNA from three species of endemic Hawaiian butterflyfishes (Chaetodon multicinctus, n = 280; Chaetodon miliaris, n = 408; Chaetodon fremblii, n = 358) sampled from across the Hawaiian Archipelago was used in a suite of population genetic analyses to examine population histories and calculate coalescence times. We review a recent phylogenetic hypothesis for the Chaetodontidae and optimize ancestral distributions to nodes as a means of inferring colonization pathways to Hawaii. Results We found no evidence for population subdivisions across their ranges for any of the three endemic Hawaiian butterflyfish species (Φ_ST ≈ 0; P > 0.05 in each case). Coalescence analyses revealed that C. multicinctus, C. miliaris and C. fremblii date to genetic bottlenecks of c. 12 ka (95% confidence interval of τ, 0–46,732 years ago), c. 74 ka (95% confidence interval of τ, 62,918–105,699 years ago) and c. 301 ka (95% confidence interval of τ, 88,981–478,495 years ago), respectively. We found that the West Pacific appears to be the ancestral source for two of three independent colonization events to Hawaii (leading to the speciation of C. miliaris and C. fremblii). The third colonization of Hawaii (leading to the divergence of C. multicinctus) is ambiguous, but may have involved island‐hopping from the South Pacific via the Line Islands. Main conclusions Our results are consistent with the growing body of data indicating that ecological specialists may be more susceptible to severe population bottlenecks during large‐scale climatic variation on evolutionary time‐scales. The isolation of the Hawaiian Archipelago presents challenges for colonization by even the most highly dispersive marine organisms, and routes of colonization by endemic butterflyfishes show a variable pattern, indicating that there may be several pathways, both spatially and temporally, for marine fauna to colonize Hawaii. Hawaiian endemic butterflyfishes appear to represent genetically homogeneous populations across the archipelago.     

Body size and population dynamics of enchytraeids with different disturbance histories and nutrient dynamics

The population dynamics of the enchytraeid Cognettia sphagnetorum originating from an unmanaged forest (FP), a clear-cut area (CCP) or a plot treated with birch ash (APP) and the effects of population origin on labile C and N dynamics were investigated. Twenty individuals of C. sphagnetorum were introduced in microcosms containing humus from the unmanaged forest devoid of enchytraeids and amended with sucrose, and incubated for 14 weeks. Triplicate microcosms from FP, CCP and APP treatments were destructively sampled every second week and enchytraeid population density, individual length, nematode abundance and trophic structure, humus properties and dissolved organic C (DOC) and N (DON), and NH₄–N in soil were determined. The enchytraeid body size was initially smaller in CCP and APP than in FP. The enchytraeid propagation rate was lower and individual size less variable in APP than in FP or CCP, and although enchytraeid size increased in all treatments, exponential population models indicated that APP was less stable. Nematode community was dominated by bacterial-feeders especially in the microcosms with APP. N mineralization rate was lower and DOC decomposition rate greater in APP systems. The results show that C. sphagnetorum is more sensitive to wood ash than clear-cutting, and its altered body size distribution has the potential to affect the dynamics of soluble nutrients.     

Rice domestication: histories and mysteries

Domesticated rice (Oryza sativa) is one of the world’s most important food crops, culturally, nutritionally and economically ( Khush 1997 ). Thus, it is no surprise that there is intense curiosity about its genetic and geographical origins, its response to selection under domestication, and the genetic structure of its wild relative, Oryza rufipogon. Studies of Oryza attempting to answer these questions have accompanied each stage of the development of molecular markers, starting with allozymes and continuing to genome sequencing. While many of these studies have been restricted to small sample sizes, in terms of either the number of markers used or the number and distribution of the accessions, costs are now low enough that researchers are including large numbers of molecular markers and accessions. How will these studies relate to previous findings and long‐held assumptions about rice domestication and evolution? If the paper in this issue of Molecular Ecology ( Huang et al. 2012 ) is any indication, there will be some considerable surprises in store. In this study, a geographically and genomically thorough sampling of O. rufipogon and O. sativa revealed two genetically distinct groups of wild rice and also indicated that only one of these groups appears to be related to domesticated rice. While this fits well with previous studies indicating that there are genetic subdivisions within O. rufipogon, it stands in contrast to previous findings that the two major varieties of O. sativa (indica and japonica) were domesticated from two (or more) subpopulations of wild rice.