Tabebuia rosealba (Bignoniaceae) to understand the disjunct geographic distribution of South American SDTFs based on statistical phylogeography and ecological niche modeling (ENM). We specifically tested the dry forest refugia hypothesis; i.e., if the multiple and isolated patches of SDTFs are current climatic relicts of a widespread and continuously distributed dry forest during the LGM. We sampled 235 individuals across 18 populations in Central Brazil and analyzed the polymorphisms at chloroplast  and nuclear (ITS nrDNA) genomes. We performed coalescence simulations of alternative hypotheses under demographic expectations from two a priori biogeographic hypotheses  and other two demographic expectances predicted by ENMs . Phylogenetic analyses based on median-joining network showed haplotype sharing among populations with evidence of incomplete lineage sorting. Coalescent analyses showed smaller effective population sizes for T. roseoalba during the LGM compared to the present-day. Simulations and ENM also showed that its current spatial pattern of genetic diversity is most likely due to a scenario of range retraction during the LGM instead of the fragmentation from a once extensive and largely contiguous SDTF across South America, not supporting the South American dry forest refugia hypothesis.Studies based on contemporary plant occurrences and pollen fossil records have proposed that the current disjunct distribution of seasonally dry tropical forests (SDTFs) across South America is the result of fragmentation of a formerly widespread and continuously distributed dry forest during the arid climatic conditions associated with the Last Glacial Maximum (LGM), which is known as the modern-day dry forest refugia hypothesis. We studied the demographic history of  In tTabebuia roseoalba (Ridl.) Sandwith (Bignoniaceae) is a seasonally dry tropical forest tree with disjunct distribution throughout the SDTFs of South America . Our phylogeographic inferences indicate that the current spatial pattern of genetic diversity of T. roseoalba is most likely due to a scenario of range retraction with smaller population size during the arid climatic conditions associated to the LGM, therefore, do not support the South American dry forest refugia hypothesis.Here we studied the phylogeography of i et al. ,17, whicT. rosealba in Brazil during 2011, mainly in SDTFs across Cerrado, Pantanal and Mata Atlântica biomes  throughout the geographic distribution of a biomes . Becausea biomes . SamplinpsbA-trnH trnC-ycf6 and trnS-trnG }, where N0 was the same for all scenarios, and N1 shifted among them according to our theoretical expectation  was simulated using N1 equal to 10,000 and “Both” N1 = 50,000, based on an exponentially positive population growth. The “Amazonian SDF Hypothesis” (PPPH) was simulated using N1 equal to 500 and “Range Retraction” was simulated using the smallest effective population size (N1 = 100), based on a negative population . To simuAIC) for model choice. The log-likelihood, ln(L), was estimated as the product of the height of the empirical frequency distribution at the observed value of diversity by the maximum height of the distribution. AIC (-2Ln(L) + 2K, where K is the number of free parameters, 2 for all models) was transformed into AIC weight of evidence (AICw), given by exp[-0.5(AIC–AICmin)]  , from wh pattern . AICw wag models .We used spatially explicit analysis to detect spatial patterns in observed genetic diversity in response to late Quaternary climate oscillations, for both cpDNA and ITS. Spatial expansion may lead to gradients in genetic diversity because of allele surfing during the colonization of new areas and “lead trail” expansion  by a Mantel test using ArlequinVer 3.11 [We first tested if differentiation is an effect of isolation by distance . PairwisVer 3.11 .h) and nucleotide (π) diversities, due to expansion of climatically suitable conditions. For this, we obtained the distance between each sampled population and the centroid of historical refugium, and then we performed quantile regressions of genetic parameters against this spatial distance.We used quantile regressions to analyze the relationships of climatic suitability and stability through time with genetic diversity . For thipsbA-trnH, trnC-ycf6 and trnS-trnG generated fragments of 461bp, 698bp, and 747bp, respectively. The combined data presented 1,519bp usable sites (excluding microsatellites and coding indels as one evolutionary step), 157 polymorphic sites and 37 different haplotypes for the 235 individuals of T. roseoalba. For ITS1 + 5.8S + ITS2 (ITS) we obtained a fragment of 533bp. The final alignment presented 506bp usable sites, 94 polymorphic sites and 14 different haplotypes.Amplification of the chloroplast intergenic spacers h = 0.839) than nuclear ITS (h = 0.336), but nucleotide diversity  was higher for nuclear genome  and ITS regions . Pairwise differentiation was high and significantly different from zero for most population pairs for both chloroplast and ITS regions . Population PAN had a higher mutation parameter (θ = 3.07735). Significant effect of population retraction followed by an expansion was found overall populations for both ITS  and chloroplast genome . When populations were analyzed, Fu’s neutrality test was significant for all populations (sample size > 2 and k > 1) for both ITS and cpDNA . Using the mutation rate reported above and the generation time of 12 years (RG Collevatti unpublished data) we estimated effective population size Ne = 20,817.31 . Most populations had high effective population size  for oseoalba , ~4.9 ± oseoalba .T. rosealba at LGM extends mainly over the Central-West Brazil and the Northeast toward the West  among the 60 paleodistribution maps. The exact patterns supporting either PLAH (16.7%) or PPPH (28.3%) were less frequent than “Range Retraction” classification. “Both” hypothesis (PLAH+PPPH) was also little supported (15%).T. roseoalba compared to other competing hypotheses, using either two-tailed probability or AICw criteria  and ITS .Differentiation among populations was not significantly correlated with geographic distance for both chloroplast DNA , effective population size (Ne) and haplotype (h) and nucleotide (π) diversities, especially for higher quantiles (θ and Ne showed negative relationships with suitability at 21 ka (h) diversity for chloroplast genome was not related with suitability.Quantile regressions showed clear effects of climate change on the genetic diversity of uantiles  Figs. Hoat 21 ka . Haplotyθ, Ne, h and π for ITS decreased with distances from the centroid of the refugium and higher values are associated with populations in more stable areas, where climatic suitability have been unchanged since the LGM  nor under its alternative arrangement combining both dynamics (PLAH + PPPH). Evidence from coalescent simulations and paleodistribution modeling indicate, actually, that the phylogeographic pattern of T. roseoalba is the result of a smaller geographic range at the LGM in comparison with present-day. Contrary to the originally expected by dry forest refugia hypothesis, the low haplotype and nucleotide diversity currently found in many populations of T. roseoalba is consistent with a demographic scenario of range retraction instead of a widely and continuously distributed SDTF during the LGM.Our findings from phylogeographic analyses of T. roseoalba occurs only on areas of high fertile soil, such as calcareous rocks, its range shift might have been less pronounced than other SDTF species such as T. impetiginosa [T. roseoalba toward the Amazon Basin may have been favored at local scales, being weakly or not captured in our modeling approach. Indeed, quantile regressions showed a clinal variation in the genetic diversity of T. roseoalba for ITS, as expected for range shift. Range shift may lead to spatial genome assortment due to lead edge colonization, leading to loss and gradients in genetic diversity [However, a range shift likewise the ‘Amazonian SDF Hypothesis’ (PPPH) may not be definitively disregarded. Firstly, because tiginosa . Moreoveiversity . The spriversity ,62.et al. [T. roseoalba might still be a SDTF species not universally favored by the dynamics of rivers throughout the Amazon basin. Anyway, our findings do not refute the Amazonian SDTF hypothesis (PPPH) at all, but do not support it as the most likely scenario for T. roseoalba .T. roseoalba, the phylogeography of other SDTF species such as Astronium urundeuva [T. impetiginosa [T. roseoalba populations, although ancient dispersal may have happened before population retraction at the Pre-Illinoian (see next section below).Contrary to our results for rundeuva  and T. itiginosa  show cletiginosa ,17 and atiginosa  species.tiginosa , and thetiginosa ,18,66 antiginosa . Indeed,tiginosa ). In thiT. roseoalba to Quaternary climate changes showed in the present work may evince a potential constrain to respond to future climate changes. Large effects of climate changes on geographical ranges and shift of SDTF' species are predicted elsewhere [T. roseoalba occurs only in highly fertile soils, this may hold back population migration and persistence threaten its long-term conservation.SDTFs are one of the most threaten ecosystems in the world . Althouglsewhere . BecauseT. rosealba. However, populations in more instable areas in southeastern and northwestern edges of the historical refugium  had high genetic diversity for chloroplast genome. We hypothesize that these populations at the edge of historical refugium may represent ‘stable rear edges’, i.e. relict populations that have persisted in suitable local habitats across the Quaternary glaciation cycles [Populations in more climatically suitable areas during the LGM, mid-Holocene and present-day presented higher genetic diversity suggesting that stable areas were important refugia for n cycles ,68. Diffn cycles .T. roseoalba was wider and started to shrink at the Pre-Illinoian glaciations due to the colder and drier conditions attaining its lower range and effective population size at the LGM. With the warmer and moisture conditions after the LGM, T. rosealba expanded its range, without secondary contact, evinced by the lack of gene flow. Populations of T. roseoalba were highly differentiated and both phylogenetic relationship among haplotypes and coalescent tree showed incomplete lineage sorting with populations geographically distant sharing a common ancestral. This result suggest that population of T. roseoalba were more connected before the Pre-Illinoian. Thus, the negligible gene flow among all population pairs (less than 1.0 migrant per generation) also indicates that the incongruence between the phylogenetic clades and geography may be the consequence of incomplete lineage sorting due to sundering [Results on EBSP analysis and Fu’s neutrality test also showed demographic population retraction followed by expansion. EBSP showed that a demographic retraction started at ~ 588 ka see , at the undering . In accoT. roseoalba lineages, dated from ~ 4.9 Ma. Different from T. impetiginosa, which lineages from the Southeast Brazil (SUM) first diverged at ~4.9 Myr BP [T. roseoalba lineages from central east Brazil (BRA and GSV) diverged first. Major divergences at geographical scale occurred in the Lower Pleistocene  [Our results also showed an ancient origin of  kyr BP) , but at T. roseoalba during the LGM, contrary to the expected by modern-day dry forest refugia hypothesis. Contrasting results for related SDTF species, like the congeneric T. roseoalba and T. impetiginosa, indicate that the effects of Quaternary climate changes on distribution dynamics of SDTF in South America is more complex than previously expected. Our study shows that SDTF responses to Quaternary climate changes should be species-specifically investigated, instead of considering multiple species in association or entire biomes. Finally, we showed here that phylogeographic analyses coupled with ecological niche modeling and coalescent simulations can be a very powerful framework for evaluating alternative hypotheses from individualistic species and potentially useful for disentangling mechanisms involved in the origin of the disjunct distribution of SDTFs.Our results based on coalescent simulation and ecological niche modeling strongly support a retraction in geographical range and effective population size of S1 FigMap adapted from Collevatti et al. (2012).(DOCX)Click here for additional data file.S2 Fig(DOCX)Click here for additional data file.S3 Fig(DOCX)Click here for additional data file.S4 Fig(DOCX)Click here for additional data file.S5 Fig(DOCX)Click here for additional data file.S6 Fig(DOCX)Click here for additional data file.S7 Fig(DOCX)Click here for additional data file.S8 Fig(DOCX)Click here for additional data file.S1 Table(DOCX)Click here for additional data file.S2 Table(DOCX)Click here for additional data file.S3 Table(DOCX)Click here for additional data file.S4 Table(DOCX)Click here for additional data file.S5 Table(DOCX)Click here for additional data file.S6 TableFST below diagonal and nuclear ITS above diagonal.Chloroplast (DOCX)Click here for additional data file.S7 TableMigration direction is from populations in the columns into populations in the rows.(DOCX)Click here for additional data file.S8 Table(DOCX)Click here for additional data file.S9 Table(DOCX)Click here for additional data file.


Homo sapiens. The paucity of African fossils remains a serious stumbling block for exploring some of these issues. However, fossil and archaeological discoveries increasingly clarify important aspects of our past, while breakthroughs from genomics and palaeogenomics have revealed aspects of the demography of Late Quaternary Eurasian hominin groups and their interactions, as well as those between foragers and farmers. This paper explores the nature and timing of key moments in the evolution of human diversity, moments in which population collapse followed by differential expansion of groups set the conditions for transitional periods. Five transitions are identified (i) at the origins of the species, 240–200 ka; (ii) at the time of the first major expansions, 130–100 ka; (iii) during a period of dispersals, 70–50 ka; (iv) across a phase of local/regional structuring of diversity, 45–25 ka; and (v) during a phase of significant extinction of hunter–gatherer diversity and expansion of particular groups, such as farmers and later societies (the Holocene Filter), 15–0 ka.The evolution of modern humans was a complex process, involving major changes in levels of diversity through time. The fossils and stone tools that record the spatial distribution of our species in the past form the backbone of our evolutionary history, and one that allows us to explore the different processes—cultural and biological—that acted to shape the evolution of different populations in the face of major climate change. Those processes created a complex palimpsest of similarities and differences, with outcomes that were at times accelerated by sharp demographic and geographical fluctuations. The result is that the population ancestral to all modern humans did not look or behave like people alive today. This has generated questions regarding the evolution of human universal characters, as well as the nature and timing of major evolutionary events in the history of This article is part of the themed issue ‘Major transitions in human evolution’. Early evolutionary models sought answers in the regional differences in Pleistocene hominin morphology to account for contemporary differences among human groups ,2. TheseNevertheless, the 200 000-year-old history of the species remains only patchily known, with a poorly mapped African origin, and shaped by major geographical and demographic expansions after 130 ka, when modern human populations began to disperse first across Africa and later into Eurasia ,17. ThisThe combined effects of population growth and population-specific biological change, including the localized admixture with other Late Quaternary hominins, led to the substantial increase in human diversity through the history of the species. Countering that long-term trend, the extinction of many small populations, each of which carried unique characteristics, has removed diversity from the species pool at particular times. The interplay between added and lost variation shaped the distinctiveness of groups through time, strengthening and weakening population boundaries. This is particularly important in the early part of the process, when the deeper structure of human diversity became established .Figure Homo sapiens is constrained by the limited number of African fossils, both before and after the out-of-Africa dispersals. This means that it is impossible at present to contrast the morphology and behaviour of the first humans in Eurasia with that of their African ancestors and immediate relatives, and thus to interpret the processes that shaped human adaptive responses to environmental expansion and/or contraction. Nevertheless, much is known about the non-African part of the human story, and ancient genomics is offering major new insights into changes in population size and relationships of early Eurasian human groups [However, any attempt at modelling the history of n groups –23, incln groups ,15,24,25n groups –28 is beThe integration of morphological, archaeological and genetic information offers the fullest picture of the pattern of human diversification, as well as insights into some of the processes involved, such as inter-group admixture. However, in order to test current interpretations of population relationships, as well as help frame questions about the environmental and competitive conditions that underlie significant moments in the history of the species, it is necessary to build a theoretical framework that places major changes in the biology and behaviour of the species, as well as changes in population size, distribution and mobility, in ecological and geographical context. Such changes were continuous, complex and dynamic. However, because climate change was not homogeneous through time, there were periods of greater stress on survivorship and of greater opportunity for population growth. Some of these periods represent transformative moments, shaped by the interplay between the loss of variation through extinction of some populations and the gained variation through the expansion of others. This paper proposes five periods of transition in the evolutionary history of our species, and explores their consequences on levels of diversity.2.Homo sapiens has long been characterized as ‘polytypic’ because of the extent of differences among populations. Nevertheless, there has been much debate about the nature and extent of human ‘polytypism’. The rate and degree of differentiation of a population is affected by five factors: (i) the demographic conditions (population size and structure), which determine the potential for drift, both at the point of separation from an ancestral source and through time; (ii) private selective forces resulting from the stress on individual survivorship and fertility in particular environments and not present elsewhere (i.e. selection acting on only one population of the species); (iii) levels of isolation that, by counteracting the homogenizing effects of gene flow, lead to inter-population diversity; (iv) levels of intra-population gene flow that promote the spread of individually acquired novelties; and (v) the time elapsed since separation from an ancestral source. Therefore, what determines the intra- and inter-population levels of diversity within the species is a combination of history, geography and demography—in other words, the evolutionary geography of the species and its populations.Human diversity is defined by the sum of unique biological and cultural variation within our species. Evolutionary geography is the branch of biology that investigates the role of spatial factors in the evolutionary process . It inveIn the case of human evolution in the Pleistocene, when hominins became transcontinental, spatial differences in environmental conditions and the geographical distance between populations became the main contexts for adaptive and neutral evolutionary change. Therefore, in order to explore whether there are particular transformative periods in the evolutionary history of humans, it is critical to understand the relationship between geography and the other two evolutionary dimensions of populations—demography and their duration as distinct entities, from the moment of founding or separation from the ancestral source to their disappearance either by extinction or by reintegration into the ancestral or another population. The backdrop of these relationships is climate change.The role of climate in evolution has been a matter of debate, from those who see climatic change as a sufficient and necessary cause for evolutionary change , to thosAlthough human population size has increased exponentially since the origin of the species, particularly, in the last 10 000 years , currentSeveral factors promote the differential success of populations following a period of contraction—the same climatic change will cause very different patterns of environmental deterioration across regions, leading to localized areas of endemism (refugia) and depopulation, the latter offering niche opportunities to the former upon recovery. Furthermore, environmental recovery is not simultaneous at regional and continental scales, so even among groups who survive periods of adversity, population expansion will begin among some before others. Finally, different ecological circumstances promote different adaptive strategies, whether biological or cultural, some of which can make a population's capacity for resource exploitation greater than others. Thus, the particular interactive effects between population collapse and expansion following a rapid shift from environmental adversity to recovery set the conditions for the periods of transition in the evolutionary history of modern humans.origins of the species, 240–200 ka; (ii) at the time of the first major expansions, 130–100 ka; (iii) during a period of major dispersals, 70–50 ka; (iv) across a phase of multiple extinctions/expansions of local/regional expression leading to the structuring of diversity, 45–25 ka; and (v) during a phase of significant extinction of hunter–gatherer diversity and expansion of particular groups, such as farmers and later societies (the Holocene Filter), 15–0 ka.I have identified five phases in which extinction and contraction are followed by significant differential expansion, and thus set the conditions for a shift in human diversity, the basis for an evolutionary transition—(i) at the 3.H. sapiens, when populations changed, dispersed or became extinct at a greater rate than others, it is necessary to consider the constraints that limit their identification. Any attempt at establishing the pattern and process of the evolution of human diversity is hampered by the incompleteness and complexity of the information, and as the fossil record increases and more ancient genomes are described, the transitions described here will become more precise and probably more numerous. Nevertheless, identifying these transitions is a critical step in developing a comprehensive model for the evolution of human diversity.Before discussing such transitions in the evolutionary history of (a)H. sapiens remains largely unknown. African Middle Pleistocene hominins share morphological and archaeological characteristics with European remains [sapiens hypodigm [The early history of  remains ,38, refl remains . This sh remains . Subsequ remains ,14,40,41 remains , but arehypodigm ,43, and hypodigm ,45. On thypodigm , and suphypodigm ,48. Howehypodigm , while ahypodigm , archaeohypodigm  and genehypodigm , althoughypodigm .H. sapiens [The archaeological record of modern human origins is complex. All early modern human fossils have been found in association with Middle Stone Age (MSA) lithic traditions, but the MSA pre-dates the earliest known fossils of  sapiens . Further sapiens , while a sapiens . The comca 200 ka) is consistent with genetic estimates of the last common ancestor of living humans based on mitochondrial DNA (mtDNA) [sapiens morphological clade, defined from the point when modern human uniquely derived traits first appear in the fossil record, pre-dates the last common genetic ancestor of living people. Thus, in the absence of a fuller late Middle Pleistocene African fossil and archaeological record, the spatial and demographic parameters of early modern human evolution in Africa remain unclear. This is critical, as the geographical location and ecological context of the ancestral population shaped the potential for drift and the selective environment under which a modern human phenotype evolved [A date for the origins of the modern human lineage at the end of MIS 7 ( (mtDNA) , but sli (mtDNA) ). Althou evolved ,56, and (b)The period between 128 and 72 ka corresponds to a long and complex interglacial (MIS 5) , which bBesides the clear change in population size evidenced by the number and distribution of archaeological sites throughout Africa, this phase of modern human evolutionary history (from the beginning of MIS 5 128 ka) to the end of MIS 4 (60 ka)), represents a moment of important behavioural innovations—the first evidence for personal ornaments ,82–86, f ka to thThe recent discovery of modern human teeth dated to approximately 80 ka in China  indicate(c)A very large proportion of living people, both in Africa and outside the continent, share a common ancestor estimated to have lived at the end of MIS 5 or during the early phases of the subsequent glacial phase, MIS 4. Genetically, this ancestor is identified as the population that gave rise to mtDNA haplogroup L3 and descendant lineages, today found across most of Africa and throughout the rest of the world ,101. In Taken together, this evidence indicates that, by the second half of MIS 5, (i) African populations were structured into different groups, consistent with the prehistoric evidence for regional differentiation and deteriorating climatic conditions; (ii) that one of these groups (‘X’) underwent sequential waves of expansion that led first to the establishment of descendant populations within Africa, creating the north–south cline of matrilineal relatedness in this group; (iii) that one of the descendant groups expanded out-of-Africa (‘X-ooA’), came into contact with Neanderthals, and assimilated some Neanderthal individuals into the group ,105; andThe pattern of population dispersals in Eurasia between 70 and 50 ka is being revealed by ancient genomics. A series of studies have shown that non-African human diversity has its genetic roots in the early splitting of groups from the ‘X-ooA’ ancestral population, leading to the establishment of a population ancestral to Australo-Papuans, one ancestral to the people of Western Asia, and one ancestral to all other groups, which divided relatively quickly into one population that gave rise to Western Eurasians and another to Eastern Eurasians ,20,22,23What is known about African populations at this time suggests different regional trajectories, consistent with observed environmental differences . In sout(d)The evolutionary history of human populations in Eurasia between 50 and 15 ka is relatively well known. The record shows that between 55 and 45 ka, modern human populations were present in western Asia , easternThis is the critical period that shaped non-African diversity, when local patterns of extinction/survivorship magnified the differences acquired during the process of population dispersals of the preceding phase and created the basal inter-population structure among non-Africans, magnifying the differences acquired during the process of population splitting in the preceding phase. Besides the signature of an ancestral admixture event with Neanderthals ,10, someThe archaeological record of the last glacial period in Africa shows the major change from the MSA to the LSA throughout the continent. Only a handful of fossils, widely separated geographically and temporally, are known from this time . Among tThe Last Glacial Maximum  was a g(e)The last deglaciation was a staggered process. The melting of the northern hemisphere glaciers, caused by an increase in northern summer insolation 20–19 ka, resulted in a rapid rise in sea-level; this was followed by the onset of deglaciation of the West Antarctic Ice Sheet between 15 and 14 ka , causingThe first phase of the process corresponds to the expansion of some hunter–gatherer–fishers from localized refugia across vast spaces newly created by abrupt climate change. In Africa, the forests expanded, the southern Cape coastline contracted and an extensive hunting–fishing population and/or trading network spread from the northern Kenyan lakes to the Nile, across the Sahel and into the greening Sahara ,125. AcrThis massive expansion of hunter–gatherers led, for the first time, to the occupation of all regions and environments of the world with the exception of Polynesia and Micronesia. In west, south and east Asia, where these expansions occurred within relatively bounded areas, population density and distribution affected mobility, leading to economically intensive foraging strategies that included cereal processing, fishing and semi-sedentism, and eventually farming. Hunting and gathering as a mode of subsistence was almost entirely replaced throughout the world in the course of the last 10 000 years. Economically, hunter–gatherers followed several different strategies, including different levels of reliance on big-game versus small-prey hunting, forest animal produce (including bee-keeping and bird-catching), fishing and shell-fishing, key plant produce (such as particularly nutritious nuts) and levels of storage, with increasing evidence for the use of fired clay pots in hunter–gatherer archaeological contexts ,122,123.Farming and animal husbandry removed one of the biggest dangers of a hunter–gatherer lifestyle—its unpredictability. By relying on resources that could be controlled in terms of amount, reproduction and storage, they reduced the threat of famine and the need for large foraging territories. The development of carbohydrate-rich and dairying diets allowed for early and reliable weaning of infants, and various studies show that traditional farmers have lower infant and child mortality than hunter–gatherers today . The ineThe extent to which expanding farmers replaced or assimilated hunter–gatherers has been a matter of dispute for decades ,133. TheAlthough the biological consequences of Holocene population movements and expansions are complex and reticulated, the impact of this process on the cultural landscape today is profound . Languag4.The diversification of modern humans was, necessarily, a gradual and continuous process. However, as briefly outlined above, the rate at which population change took place was different across space and, especially, across time. Major changes in the biology and/or behaviour of human populations follow from periods of intense selection and/or drift, when pressure on survivorship was a major challenge, or from periods of rapid population growth, when biological and cultural novelties accompany demographic expansion. In evolutionary terms, transitions often conflate both mechanisms. The biological and/or behavioural changes that take place during population collapse are only revealed if the group survives, and particularly if it subsequently expands demographically, and thus magnifies the differences acquired during the period of increased drift, to which the novel variation due to population growth is added. However, not all populations survive severe bottlenecks, or recover from one at the same rate. In the first case, when small groups become extinct, the areas left vacant fuel the pace of expansion of neighbouring groups when conditions improve; in the second case, when demographic recovery is slow, the scope of success depends on the distance from the wave of expansion of others. The result is that periods of rapid population growth of some groups are also associated with the extinction of others, acting like a filter. Therefore, transitions result from the interaction between (i) the addition of variation during population collapse and rapid expansion and (ii) the loss of variation due to localized population extinction and/or their partial assimilation into expanding groups. These transitions are thus the moments when the level, distribution and structure of diversity in the history of modern humans changed significantly .Figure Origins: 240–200 ka (MIS 7), Africa. This transition involves the evolution of the distinct, universal morphological traits of H. sapiens, and characterises the change from archaic to modern morphology in one African lineage. The size of Africa, together with the paucity of fossils and securely dated archaeological sites, precludes establishing patterns of population extinction/assimilation at this time. Thus, the chronological and spatial framework for the disappearance of ‘archaic’ African populations is unknown, although the late survivorship of non-current combinations of morphological traits and rare ancient genetic lineages, supported by the apparent ‘ragged’ disappearance of MSA technologies, suggests modern human hegemony in Africa is relatively recent. With only a handful of fossil crania between 200 and 12 ka [Structuring phase, when a combination of human population growth, shown by the number of LSA sites across the continent, and climate adversity may have led to their final extinction.(1) nd 12 ka , and no Expansion: 130–100 ka (MIS 5), Africa, with Eurasian incursion. This transition follows a major glacial period, during which hominin and human African populations would have become fragmented and diversified through drift and adaptation. Little is known about this process, but the subsequent modern human expansion is shaped by a strong shift in demography and behaviour, and leads to the establishment of discrete regional populations of H. sapiens across southern, eastern and northern Africa, the probable assimilation of individuals from archaic African groups in these regions, as well as the temporary occupation by humans of the Levant, possibly Arabia and south Asia, with descendant populations as far as China. The outcome of this transition was the structuring of African populations, including the population ancestral to a large portion of Africans and all non-African groups.(2) Dispersals: 70–50 ka (MIS 4–3), Africa, Eurasia and Oceania. In eastern Africa, this period follows the end of a megadrought, when populations would have expanded as ecological conditions improved. One of these populations would have given rise to the Eurasian dispersals that characterise this period. In both southern and northwest Africa, local populations flourish until approximately 60 ka, when a period of decline is suggested by the archaeological record, while in east Africa, this phase marks the origins of the LSA. Out of Africa, this phase takes the form of an adaptive radiation, with a major expansion of populations that, by the end of the period, have colonized vast areas of Asia and reached the Sahul landmass. This critical period is extremely poorly represented in the fossil record of the species, and most of what we know about it in Eurasia derives from genetic and genomic inferences.(3) Structuring: 45–25 kyr (MIS 3–2), Africa, Eurasia and Oceania. This is the phase in which the conditions of the preceding expansions end, some populations become extinct, others progressively fragment, and inter-group diversity increases. The main structure of living human diversity is established during this phase, with the formation of regional patterns that have been ‘re-shuffled’ since. It also corresponds with the period of extinction of Eurasian archaic populations.(4) The Holocene Filter: the last 15 000 years (MIS 2–1), global. This transition is the outcome of a sequence of events, from the extinction of populations during the LGM, to the subsequent differential and asynchronous expansion of hunter–gatherers, farmers and more recent groups creating a layered process in which the species diversity changed through the loss of inter-group diversity (some dating to the origins of the lineage) and the gain of diversity by large population growth.(5) Using the evidence outlined above, I have identified five such transitions in the history of modern humans:5.Given the paucity of information about the Late Quaternary African record, as well as the complex spatial and demographic patterns of global human diversification, the identification of key periods in which the level and distribution of human diversity changed significantly provides a working model for exploring the climatic, ecological and demographic factors that shaped human biological and cultural adaptation. Some of these adaptations are global, and must lie at the root of human resilience and success; others are continental and reflect the features that promoted major geographical expansions into novel territories, while yet others are recent and regional, and reflect local change, migration and assimilation of indigenous groups. Together they define a hominin species that is phylogenetically, spatially and demographically unique.


Fst estimates for conservation flocks were moderate to high with a maximum reached between VD_C and VD_F (0.285). However, Fst estimates for field population were excessively low between the NN_C and EC_F (0.007) and between EC_F and OV_F (0.009). The significant population differentiation of the conservation flocks from their geographically correlated field populations of origin is further supported by the analysis of molecular variance (AMOVA), with 10.51 % of genetic diversity ascribed to population differences within groups (FSC = 0.106). The results suggest that significant genetic erosion has occurred within the conservation flocks due to inbreeding, pronounced effects of random drift and selection. It might be necessary to introduce new breeding individuals from the respective field populations in order to increase the effective population sizes of the conservation flocks and counter the effects of genetic erosion.Conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. Therefore, the Agricultural Research Council of South Africa initiated a conservation programme for four South African indigenous chicken breeds. The evaluation and monitoring of the genetic constitution of these conservation flocks is important for proper management of the conservation programme. Using molecular genetic analyses, the effective population sizes and relatedness of these conservation flocks were compared to village (field) chicken populations from which they were derived. Genetic diversity within and between these populations are further discussed within the context of population size. The conservation flocks for the respective breeds had relatively small effective population sizes (point estimate range 38.6–78.6) in comparison to the field populations (point estimate range 118.9–580.0). Furthermore, evidence supports a transient heterozygous excess, generally associated with the occurrence of a recent population bottleneck. Genetic diversity, as measured by the number of alleles, heterozygosity and information index, was also significantly reduced in the conservation flocks. The average relatedness amongst the conservation flocks was high, whilst it remained low for the field populations. There was also significant evidence for population differentiation between field and conservation populations. The online version of this article (doi:10.1007/s11250-016-1030-9) contains supplementary material, which is available to authorized users. In recent years, there have been particular concerns raised regarding the adaptability and evolutionary potential of highly industrialised livestock breeds, considering global climate change and food security , as well as moderately high Fis estimates (between 0.21 and 0.35), suggesting possible inbreeding. On the contrary, Mtileni et al.  between the two studies. Both studies also supported significant population substructure between the various conservation flocks, but this was more evident in the study by Mtileni et al.  using the resource flocks held for conservation. Van Marle-Köster et al.  reportedi et al.  reportedi et al. .Nes. Furthermore, this effective population size analysis will also take into account not only the current census size of a population but also the history of the population. This study, therefore, aimed to evaluate the intra- and interpopulation genetic diversity of these flocks within the context of demographic dynamics  and inbreeding, in particular, the possibility of a recent population bottleneck, creating a transient heterozygous excess, deflating the Fis estimates and consequently leading to under-estimation of true levels of current inbreeding.To formulate appropriate managerial strategies for these indigenous chickens and to prevent genetic erosion, it is necessary to assess the causality of such discrepancies. Effective population size has been used as a criterion for determining the extinction risk and for setting conservation limits (CLs) of single populations (and/or species), e.g. in international guidelines for categorising threatened species (Mace and Lande n = 30), Ovambo , Naked Neck  and Potchefstroom Koekoek . For comparison, a random sample of village chickens from three South African provincial regions was also taken: Venda , Ovambo  and the Eastern Cape Province . Village chicken populations were sampled from farming areas from which the current conservation flocks originated, which are Limpopo Province (VD_F chickens) and Northern Cape Province along the border with Namibia (OV_F chickens) as well as the Eastern Cape Province (EC_F chickens). Ninety-eight households were randomly selected from 23 villages of Vhembe and Mopani Districts in the Limpopo Province, Kgalagadi and Namaqua Districts of the Northern Cape Province and Alfred Nzo and OR Tambo Districts of the Eastern Cape Province. For each district, 2–5 villages were selected. The distance between villages within district ranged from 20 to 40 km, 100 to 500 km between districts within a province and over 1000 km between provinces. One chicken was sampled per household. Blood was collected from the wing vein onto FTA micro-cards  for each individual. A standard phenol/chloroform extraction protocol was followed for DNA isolation   and expected heterozygosity (He), number of alleles (An), effective number of alleles (Ae) and the information (Shannon-Weaver) index (I). To test whether there were significant differences in diversity between the village (field) chickens and the conservation flocks a Kruskal-Wallis test was performed  in XLStatistics v.10.05.03  and a locus-by-locus hierarchical analysis of molecular variance (AMOVA)  was calculated in Arlequin v.3.5.1.2 , population contractions or expansions] and inbreeding, in particular, the possibility of a recent population bottleneck, creating a transient heterozygous excess, deflating the Fis estimates and consequently leading to under-estimation of true levels of current inbreeding. In general, tables and figures summarise the analysed data. There was no evidence for large allele dropout or excessive stuttering that could have influenced allele scoring. However, eight loci demonstrated genotypic patterns consistent with the presence of null alleles  in one or more populations, and these loci were removed from further analyses. The remaining 21 loci are all in Hardy-Weinberg expectations (P > 0.01), and none were identified as outliers in the Fst outlier test and were thus presumed selectively neutral. Estimates of genetic diversity were low to moderate across the populations. The VD_C population consistently demonstrated the lowest genetic diversity across all measures , whilst the OV_F and EC_F populations showed the highest levels of genetic diversity . The low genetic diversity in these conservation flocks was previously confirmed  amongst the conservation flocks were significantly higher than for the field populations, suggesting considerable inbreeding , with smaller estimates for the conservation flocks (point estimate range 38.6–78.6). Both methods of estimation showed that the NN_C and VD_C populations had the smallest Ne , which in turn is often assumed to be a function of inbreeding , which is generally required for maintaining a viable population . However, pairwise Fst estimates between the NN_C and EC_F and between EC_F and OV_F were excessively low  (Table FSC = 0.106) (Table FCT = 0.006) failed to reach statistical significance probably due to the low degree of population differentiation of the field populations  Table  and 4. T6) Table  and the 6) Table . The varns Table . The lonns Table .Table 2In conclusion, there is sufficient evidence to suggest that the current conservation flocks kept at the Poultry Breeding Resource Unit of the Agricultural Research Council (South Africa) are genetically distinct from the village chickens from where they were sourced originally. These conservation flocks represent small and isolated populations with relatively high levels of inbreeding and genetic erosion. Results from the current study raise some concerns with regard to the long-term sustainability of the conservation programme. Furthermore, there is evidence suggesting that the conservation flocks have undergone a recent bottleneck that is not associated with the original founder event in 1994. This bottleneck could be due to selective breeding to enhance the productivity of these indigenous breeds. It may, therefore, be advisable to maintain separate, but connected programmes for conservation and genetic improvement. As such, the conservation programme may feed into the genetic improvement programme, but preserving genetic diversity within the conservation nucleus populations must be prioritised in order to ensure population adaptability and resilience in the aim of future breeding objectives. Therefore, it may be advantageous to augment the current conservation flocks with individual animals from geographically correlated populations in an effort to restore lost genetic diversity and negate the adverse effects of small effective population sizes and inbreeding.ESM 1(DOC 103 kb)Below is the link to the electronic supplementary material.


Anopheles (Nyssorhynchus) darlingi Root, which primarily inhabits rainforest. To test this biogeographical hypothesis, we analyzed 786 single nucleotide polymorphisms (SNPs) in 12 populations of An. darlingi from across the complex Brazilian landscape. Both model-based (STRUCTURE) and non-model-based  analysis of population structure detected three major genetic clusters that correspond with newly described Neotropical biogeographical regions: 1) Atlantic Forest province (= southeast population); 2) Parana Forest province ; and 3) Brazilian dominion population (= Amazonian population with one Chacoan population - TO). Significant levels of pairwise genetic divergences were found among the three clusters, allele sharing among clusters was negligible, and geographical distance did not contribute to differentiation. We infer that the Atlantic forest coastal mountain range limited dispersal between the Atlantic Forest province and the Parana Forest province populations, and that the large, diagonal open vegetation region of the Chacoan dominion dramatically reduced dispersal between the Parana and Brazilian dominion populations. We hypothesize that the three genetic clusters may represent three putative species.The major drivers of the extensive biodiversity of the Neotropics are proposed to be geological and tectonic events together with Pliocene and Pleistocene environmental and climatic change. Geographical barriers represented by the rivers Amazonas/Solimões, the Andes and the coastal mountain ranges in eastern Brazil have been hypothesized to lead to diversification within the primary malaria vector,  Anopheles (Nyssorhynchus) darlingi Root is broadly distributed in Central and South America, extending from southeastern Mexico to northern Argentina and from east of the Andes to the Atlantic coast [An. darlingi is associated with malaria dynamics in forest areas where the natural ecosystems are undergoing intensive ecological changes promoted by deforestation and land use [ic coast . This spland use , 3.Anopheles darlingi was described by Root [Anopheles paulistensis Galvão, Lane and Corrêa was described as a morphological variant of An. darlingi based on differences in the egg, male and female morphology of specimens from Pereira Barreto, inland São Paulo state and Manaus, Amazonas state [An. paulistensis was synonymized with An. darlingi. Polymorphisms were also observed in the banding pattern of the X and all four autosome arms of the salivary gland polytene chromosome of representatives of An. darlingi populations from three northern localities in the Amazon forest and one southern locality in the domain of Cerrado, inland São Paulo state, and considered to be linked with distinct vectorial capacity [COI) [An. darlingi has been considered to be a monotypic species based on other data sets [ by Root  based on by Root  expandedas state . Later, as state  considercapacity . More recapacity  observedcapacity . Furthercapacity , 10, in capacity , in vectcapacity , and in ty [COI) , and micty [COI) . In contata sets , 16.An. darlingi, COI sequences [COI split [Using specimens spanning almost the entire distribution of equences  and micrequences  detectedOI split ; in contOI split .COI resolved two genetic clusters that coincide with two centers of endemism: 1) within the Amazonas/Solimões river basin plus Guyana (north of the Amazon), and 2) within South America , with expansions that occurred during the Pleistocene [An. darlingi was not homogeneous [Within South American populations, variation in istocene . Subsequogeneous . Geograpogeneous . It is wAn. darlingi from the southeastern and inland Atlantic Forest differ substantially, and hypothesized that the major geographic barrier represented by the coastal mountain range limited the dispersal of populations across the Atlantic Forest.The Atlantic Forest, originally approximately 150 million hectares, is one of the largest tropical rainforests in the Americas. Its extreme latitudinal dimension (about 29 degrees) and an altitudinal span from sea level (Atlantic coast) to ~2800m (Serra do Mar and Serra da Mantiqueira), incorporates tropical and subtropical zones with diverse environmental conditions . The varAn. darlingi populations may be attributed to biogeographical events that delineated the Neotropical region. We hypothesize that the development of the open vegetation area comprising the Chacoan dominion, also known as the Chaco, Cerrado and Caatinga biomes, is one of the primary isolating mechanisms that promoted the genetic differentiation of An. darlingi population groups  proposed by Pedro and Sallum [The Neotropical region consists mainly of forest biomes, with some extensive open vegetation biomes along a wide diagonal that comprises the Pampa, Chaco, Cerrado and Caatinga provinces . Graduald Sallum .An. darlingi [An. darlingi throughout Brazil; 2) address how genetic diversity is distributed between and within the major forest domains of Amazonia and Atlantic Forest compared with Cerrado; 3) examine whether divergence among population subgroups from the Atlantic coast and central Amazonia, southern and northeast Brazil [An. paulistensis and An. darlingi; 4) address the hypothesis that the Amazonian population represents an unknown putative species; and 5) discuss patterns of structure in the context of Neotropical biogeographical regionalization [Herein, we use genotyping by sequencing with nextRAD  markers  to detect SNPs, which increase marker-resolution approximately three orders of magnitude compared with previous population genetic studies in darlingi , 24, 25.t Brazil , are conlization .An. darlingi were chosen from field collections in twelve states in Brazil  to Maria Anice M. Sallum and E. S. Bergo. Specific permission was not required for these loca- tions as permission to collect was granted under the permanent permit. The collection locations were not privately owned or protected in any way. The field studies did not involve protected or endangered species.Mosquitoes were captured either as larvae/pupae or adults. Males and females were collected using Shannon traps. Both adults and immature stages were sampled from multiple habitat types, such as riverside, lakeside, large farm, natural reserve and agricultural settlement, to maximize within region heterogeneity and to reduce the risk of collecting related individuals, particularly in larval habitat.Genomic DNA was extracted (Qiagen DNAEasy kit) from 57 individual mosquitoes  represenAn. darlingi genome using bowtie [K for our samples, we used the Evanno method [Raw Illumina sequences (NCBI SRA Accession numbers SRS950393-SRS950449) were processed with STACKS v1 , 28. Brig bowtie . The refg bowtie  for K vao method  implemeno method . A complo method  and AMOVo method .Due to the possibility of bias introduced in model-based  analyses, particularly due to relatively low numbers of sequences at each locus, we also implemented a Discriminant Analysis of Principal Components (DAPC) , implemeAn. darlingi reference genome [An average of 1,625,745  101bp, Illumina reads were aligned to the e genome  and resuThere is no evidence of isolation-by-distance among the 12 populations surveyed  that cover a range of 219 to 3,059 km. Therefore we used STRUCTURE , PrincipAn. darlingi in Brazil  cluOnce this initial level of population structure was assessed, the genotype dataset was further filtered in order to minimize the possible bias on population genetic inferences due to missing genotype data . The majSTRUCTURE analysis of the filtered SNP dataset discriminated three distinct genetic clusters as outlined above . There wPrincipal Components Analysis (PCA) showed clear partitioning of the populations in the first two principal components . The firIn the DAPC analysis, there was no clear ‘best’ value for the number of clusters, with the Bayesian Information Criterion (BIC) value for one, two, or three clusters, being very similar . Therefost = 0.20, P < 0.001) with the highest genome-wide divergence between the southeast and West Atlantic populations: southeast population—West Atlantic population , southeast population—Amazon population , and West Atlantic population—Amazon population . There was also significant level of genetic divergence between the multiple Amazonian populations as compared with the non-Amazonian populations .There were significant levels of pairwise genetic divergence among the three clusters . Fo. FoAn. do & Conn , studyino & Conn , 25 and o & Conn , microsao & Conn , by inclo & Conn . Even tho & Conn , Angêllao & Conn  identifiAn. darlingi populations and to test whether clusters are consistent with well-separated species. Analyses of the genome-wide data showed that individuals group into three genotypic clusters. Cluster 1 (red) comprises populations from the Atlantic Forest province  of the Parana dominion, representing An. darlingi. Cluster 2 (green) includes representatives from localities within the Parana Forest province of the Parana dominion  with one Cerrado province population (Chacoan dominion). Cluster 3 (blue) incorporates the Boreal Brazilian and South Brazilian dominion populations (with one Cerrado province population)  cruzii, such that different putative species have evolved [An. darlingi) and 2 (putative An. paulistensis).Several approaches were employed in the present study to address genomic variation among ulation) . Thus, tulation) , and on bregions , we prop evolved , 45. ThiCluster 3 populations represent the Boreal Brazilian dominion  and South Brazilian dominion  both within the Brazilian subregion; in addition, this cluster includes individuals from the Cerrado province (TO) of the Chacoan dominion. There is a low level of allele sharing between clusters 2 and 3. One of these individuals is from Cerrado province (TO) population and the other sample is from Madeira province (MT) . The shaAn. darlingi, based on Morrone [b gene, observed that small forest-dwelling mammals distributed between and within the major forest domains of the Amazonia and Atlantic Forests and the intervening interior forest of Brazil diverged significantly. Between sister taxa of Neotropical orchard bees, Silva et al. [Manikara, the divergence between Atlantic coastal forest and Amazonian clades coincided with the formation of drier Cerrado and Caatinga habitats between them [Hypsiboas albopunctatus from the central Cerrado was found to have diverged from a southeastern clade (Brazilian Atlantic Forest) during the mid-Pleistocene [If our inference for  Morrone , 26 of p Morrone , using da et al.  found theen them . A cladeistocene . Soil miistocene .Polietina (Diptera: Muscidae) from the Neotropical region. The fact that the An. darlingi population from Tocantins state  clustered with populations from the South Brazilian dominion may be a consequence of phylogenetic and biogeographical patterns that promoted the division of the forest biomes of the Neotropical region into the main components postulated by [An. darlingi population of the Cerrado province (Chacoan dominion) did not cluster together but split into two clusters representative of the Brazilian dominion (cluster 3) and Parana plus Chacoan dominions (cluster 2). Alternatively, our results may be a consequence of sampling strategy with only two populations from the Chacoan dominion, which did not allow a clear separation among distinct biogeographical components postulated by Morrone [In addition, Nihei and Carvalho  defendedlated by . Consequ cluster . Alterna Morrone .An. darlingi was described by Root [An. paulistensis, described by Galvão et al [An. darlingi by Lane [An. paulistensis may be a valid putative species of the subgenus Nyssorhynchus. The genetic divergence between clusters 1 and 2 and the fact that cluster 3 is equally divergent from the other two clusters could also indicate that heterogeneous divergence among populations of An. darlingi was caused by ecological selection pressures and historical biogeographical processes that may have allowed the contact and separation among distinct populations during the historical events that had led to major Brazilian biome formation.It is noteworthy that  by Root  using spão et al  from sam by Lane ; here weAn. coluzzii) and S (An. gambiae) forms, recently described as valid species, continue to differentiate [An. darlingi may shed light on the mechanisms underlying its significant vectorial capacity in the Neotropics, and also help to clarify the vector status of the species in areas outside and inside the Amazon River basin.Several recent studies have led to the discovery of heterogeneous divergence across anopheline genomes under eco-environmental selection pressure –55. Suchrentiate . FurtherS1 Fig(PDF)Click here for additional data file.S1 Table(XLSX)Click here for additional data file.S2 Table(CSV)Click here for additional data file.S1 Text(TXT)Click here for additional data file.


Paraleucilla magna is the first calcareous sponge introduced to the Mediterranean and Northeastern Atlantic. The study aimed at investigating the genetic makeup and connectivity of the introduced populations of P. magna and at exploring signs of local phenotypic adaptation, to gain insight on the species invasive potential. Ten populations along the species introduction range  were genetically characterized by using nine microsatellite markers. Most populations were genetically structured as suggested by significant Dst and Fst values, significant differences among populations (AMOVA) and the presence of private alleles. The analyzed populations belonged to three genetically homogeneous groups (K) according to the Bayesian algorithm (structure software) and the UPGMA dendrogram. Genetic diversity within populations was higher than expected. Recurrent introductions of non-randomly selected individuals from the native sources may have contributed to the heterozygote deficit found in all populations by forming pedigree structures with mating among relatives. Moreover, the species biological cycle was monitored in a population established on native Mediterranean assemblages  and compared with the species cycle in other habitats. Contrasting life spans, growth habits, and reproduction cycles, depending on the habitat conditions, were recorded. To summarize, high genetic diversity, phenotypic local adaptation, and high reproduction rates altogether allow predicting the fast proliferation of P. magna in newly colonized regions and point to its strong invasive potential.Sponges are considered poor invaders, and no genetic studies on introduced sponges have been performed up to now. The online version of this article (doi:10.1007/s00227-016-2862-6) contains supplementary material, which is available to authorized users. The ninp values of all analyses involving multiple comparisons were corrected using the False Discovery Rate (FDR) correction, which is less stringent in controlling the expected proportion of incorrectly rejected null hypothesis than Bonferroni correction and thus increases the analysis statistical power  is equal to the expected heterozygosity at mutation drift equilibrium (Heq). The excess of He over Heq is the evidence of severe reduction in population effective size that is compatible with a bottleneck or founder event  and the confidence intervals according to Manly  was performed with ARLEQUIN  and the ad hoc statistic ΔK, based on the rate of change in the log probability of data between successive K values  and the logarithm of the geographical distances between the populations .Isolation by distance was tested with a Mantel test using the correlation between pairwise genetic differentiation . Sampling periodicity was monthly, except on two occasions when the sea conditions prevented diving . For the population dynamics’ study, randomly selected, 20 × 20 cm surfaces (three replicates) were scraped to reveal the rocky substrate monthly from July 2007 to April 2008. The samples were taken to the laboratory and examined under a stereomicroscope. Calcareous sponges from 1.5 mm in size on, purportedly belonging to P. magna, were isolated and their identity confirmed by amplifying three to five species-specific microsatellites , no individual in the scrapped quadrats could be ascribed to 007 Fig. .Measuring individual height across the whole sponge cycle as an estimator of growth was a compromise solution. Height was a good proxy of increase in size for recruits and juveniles, which mainly grew up with a cylindrical shape. Although this measure was less appropriated for measuring larger irregular individuals, it also captured some growth, as irregular individuals also increased in high. Moreover, the study focused on uncovering the sponge growth during the first months after recruitment and on assessing how long the individuals took to reach their maximum size in the population, and these two goals were acceptably achieved with the measure used.The sponge life cycle was analyzed from December 2007  to July 2008. Five, ≥16 mm high, randomly selected specimens were collected monthly for detecting the presence of reproductive elements by means of histological sections and ultrastructure observations. From April 2008 (when oocytes were first detected in the sponge tissues), sampling was conducted every 15 days to capture more accurately gamete formation, embryo hatching, and larval release.Sponge samples for light microscopy were preserved in 10 % formaldehyde in seawater for 5 h and then changed to 4 % formaldehyde in seawater. Once fixed, the samples were decalcified in 5 % EDTA for 2 h and subsequently rinsed in distilled water, dehydrated in an ethanol series , cleared in toluene/ethanol 1:1 (30 min) and then in pure toluene (15 min) and embedded in paraffin before being cut in 5-µm thick sections using a Autocut 2040 Reichert-Jung microtome. After deparaffining with xylene, the sections were stained with hematoxylin and Schiff reagent. Photographs were taken with a digital camera mounted on a Zeiss Axioplan II microscope.3 in size were fixed in 1 % OsO4 and 2 % glutaraldehyde in 0.45 M sodium acetate buffer (pH 6.4) with 10 % sucrose (1:3) , to confirm the presence and the nature of the reproductive elements detected through light microscope. Samples of ca. 2 mmP. magna belonging to ten populations were genotyped for nine microsatellite primers previously designed  for all populations  were significant for all pairwise comparisons (Dest) or for all the comparisons but three (Fst), after the FDR correction . No significant differences were found between the Mediterranean and Atlantic basins or among population clusters formed according to their geographical proximity (data not shown). However, between basins and among groups differences turned out to be significant and explained 1.18 and 2.5 % of the variance, respectively (p < 0.05 in both cases), when the groups were established according to the nature of the water masses bathing the coasts of the sampling sites   according to the highest increment of k between the models with two and three groups  indicated the highest likelihood for the model with three genetically homogeneous groups of individuals  Mediterranean populations plus that of Sagres  (B) the Brazil population plus that of Port Lligat, and (C) North Atlantic insular populations (Flores and Madeira) Fig. . The Flor = 0.44, p < 0.01).The Mantel test indicated a low but significant correlation between population genetic differentiation and geographical distance . When the Port Lligat population was removed from the analysis, the correlation value increased as well as the level of significance , were first recorded in October (2007). Recruitment pursued for 3 months as recruits of the 1.5–2 mm size class were observed until December (2007) Fig.  but growOocytes (15–20 µm in size) were recorded in the sponge tissue during ca. 4.5 months (from April to July 2008), and one 15 µm in diameter spermatic cyst was observed in April Fig. . Oocyte cells in croix) were present between the larval ciliated cells , covering similar geographical ranges  ranging from 45 to 90, was higher than generally expected for a recent introduction , and the presence of private alleles, which may be caused by both the genetic drift and recurrent introductions from genetically differentiated populations within the native range. Nevertheless, the Mantel test showed significant isolation by distance, which became more significant when the Port Lligat population, genetically close to the distant population of Brazil, was removed. This isolation by distance pattern suggests that either the introductions followed a stepping stone model, which is not likely, or that the species distribution was not only man-mediated but also produced by some natural dispersal.Moreover, most populations were strongly structured as proved by significant DThe AMOVA analysis showed significant genetic differences between the Mediterranean and Atlantic basins only when they were defined as a function of the water masses (either Atlantic or Mediterranean) bathing the populations: Sagres  is under the influence of Mediterranean water masses entering the Atlantic trough the Gibraltar Strait, while La Herradura (Mediterranean) is bathed by large, tidally induced pulses of Atlantic water entering the Mediterranean , Mediterranean (including Sagres), and Port Lligat Brazil populations. The Sagres population shared alleles with those from the Mediterranean, and the same occurred between La Herradura and the North Atlantic populations.Several phenotypic characteristics of the species vary across the colonized habitats. Shape ranges from long tubes in sheltered eutrophic habitats  concomitantly with the runoff of nutrients into the seawater produced during the raining season  when most filter-feeders experience food depletion  specimens (approximated estimate) spend only three months to reach the highest size class of 100 ml (ca. 10.5 cm × 3.5 cm × 3 cm) in the eutrophic Mar Piccolo de Taranto  in well-preserved assemblages of Northwestern Mediterranean (this study), while 5 mmP. magna around shellfish farms, in particular Mytilus cultures  before P. magna was recorded in the Mediterranean Supplementary material 2 (PDF 72 kb)Below is the link to the electronic supplementary material.


Schizothorax nukiangensis, a high altitude, valuable fish species, which is distributed throughout the Nujiang River, was investigated by mitochondrial DNA sequence analysis. The cytochrome c oxidase subunit I (COI), cytochrome b (cytb), and the mitochondrial control region (MCR) of S. nukiangensis were concatenated for examination of population structure and demographic history. The concatenated data set (2405 bp) implied a pronounced genetic population structure  and defined two population units. Strong differentiation was detected between the Sanjiangkou (SJK) population and other populations due to environmental heterogeneity, dispersal ability, and/or glacial cycles. Additional DNA sequencing of the nuclear RAG2 gene also examined significant differentiation between two units and between SJK and the upstream populations (U-unit). Recent expansion events suggest that S. nukiangensis may have undergone a rapid increase during warm interglacial periods. Surprisingly, S. nukiangensis appears to have undergone an obvious expansion during the last glaciations (LG) for cold hardiness and a sharp contraction from 1.5 ka to the present. However, two population units exhibited different reflections during the LG, which might be closely related to their living habitats and cold hardiness. A clear pattern of isolation by distance was detected in S. nukiangensis due to feeding habits, limited dispersal ability, and/or philopatry. It is vitally important that more attention be given to S. nukiangensis due to low genetic diversity, lack of gene flow, and recent population contraction.Geographic distance, different living habitats or Pleistocene climatic oscillations have frequently been found to shape population genetic structure in many species. The genetic structure of  Schizothorax lissolabiatus, S. gongshanensis, S. yunnanensis paoshanensis, and S. nukiangensis) have been documented in the Nujiang River system (Chu and Chen S. nukiangensis (Cypriniformes: Cyprinidae)  Fig. is a pla Dudgeon . ConsequS. nukiangensis is distributed throughout the Nujiang River, it is an ideal candidate for the study of population genetics in a continuous model.Freshwater ecosystems all over the world have been heavily exploited and degraded by human activities, affecting both fish and fisheries; thus, it is vital that conservation efforts are undertaken quickly. Population genetic analysis is a widely used approach for assessing the genetic divergence in populations  model , cytochrome b gene (cytb), and control region (MCR)) were employed as a mitochondrial concatenated data set (MCD) to evaluate genetic diversity, the population genetic structure, and population demographic history of S. nukiangensis. Furthermore, whether IBD plays a role in shaping the structure of S. nukiangensis populations was investigated and whether the height of water acts as barrier to gene flow among S. nukiangensis populations was examined. This study seeks to develop meaningful recommendations for conservation policies and the preservation of S. nukiangensis.In this study, three mitochondrial DNA sequences , 3 μL of 10× reaction buffer, 1.5 μL of dNTPs (2.5 mmol/L each), and 2.0 U of Taq DNA polymerase in a total volume of 30 μL. The PCR conditions for COI were as follows: initial denaturation at 95°C for 5 min, followed by 30 cycles of denaturation at 95°C for 1 min, annealing at 50°C for 45 sec, extension at 72°C for 45 sec, followed by a final extension at 72°C for 10 min. The PCR conditions were identical for the cytb gene and MCR, with an initial denaturation at 94°C for 3 min, followed by 30 cycles of denaturation at 94°C for 1 min, annealing at 58–64°C for 1 min, extension at 72°C for 1 min, followed by a final extension at 72°C for 5 min. The partial nuclear recombinase activating gene 2 (RAG2) sequences were obtained from a subset of samples consisting of 33 individuals with the primers RAG2-f2a and RAG2-R6a  and aligned using the CLUSTALX 2.0 program  and haplotype diversity (h) (Nei Genetic diversities are reflected in the nucleotide diversity ( (h) Nei , and the (h) Nei . A netwo (h) Nei . The phy (h) Nei  using a  (h) Nei .N = 4), the Chenggan (CG) population was analyzed with the geographically closest population, Pihe (PH). The concatenated population was named PC and the midpoint was defined as the sample site. Pairwise genetic divergences between populations were estimated using F-statistics (FST) −1  contained 13 variable sites, 7 of which were parsimony informative. The cytb (1063 bp) had 28 variable sites, 16 of which were parsimony informative. The MCR (667 bp) demonstrated 41 variable sites, 31 of which were parsimony informative. No insertions and deletions were found in any of the three gene parts. A total of 83 haplotypes were defined among the all of the MCD sequences. For RAG2, we sequenced 33 individuals from a subset of samples selected based on the MCD haplotypes. The 1126-bp fragment included five polymorphic sites, and all sequences contained five alleles. The haplotype and allele sequences were deposited in GenBank , and nucleotide diversity (π) values within each population and in the overall population are presented in TableThe number of haplotypes, location-special haplotypes and the haplotype diversity  occurred within sampling sites (FST in S. nukiangensis was 0.149 and was significantly different from zero (p < 0.001). The largest mean FCT index was found for two populations units  referred to as follows: (1) XPT/SJK (D-unit); (2) the other six upstream populations (U-unit)    , Fig. S2< 0.001) . Similar < 0.05) . ClusterFST) ranged from −0.019 to 0.463 and are shown in TableFST among the sampling areas.Pairwise comparisons of genetic differentiation −1: R = 0.5388, P = 0.0195) −1: R = 0.2780, P = 0.1101).There was a statistically significant relationship between population differentiation and geographic distance  or by the raggedness index of the distribution  (TableThe est Table. Additioest Table. The mod81) Table. Using t81) Table. For all81) Table. A sharpS. nukiangensis in continuous habitat. Environmental heterogeneity, limited dispersal ability and /or glacial cycles may drive genetic differentiation among populations in the fine geographic scale. Because of differential living regions and cold tolerance, S. nukiangensis shows differential responses to climatic fluctuations during the Pleistocene. Considering limited sample range and molecular markers in our study, our presented hypotheses were not very strong. Therefore, more sample size and molecular markers should be employed in the future to demonstrate our hypotheses.Our study documents genetic structure and population demography within S. nukiangensis compared with S. prenanti, S. o'connori, Platypharodon extremus, and Gymnocypris chilianensis . It is also feasible that glacial cycles may have given rise to the pattern of genetic structure. Cyclic cooling potentially restricted S. nukiangensis to a number of confined regions, which impeded gene flow among populations. The end of the glacial periods would then be followed by a population expansion event and secondary admixture; however, they might not be a panmictic population after long-term isolation.In contrast to cases of absence of genetic differentiation in the schizothoracine fishes  for the overall population and U-unit population. Two reasons may account for this abnormal phenomenon. First, the habitat of S. nukiangensis might not have been covered by ice during the LG. S. nukiangensis in the current study resides at low elevation (612–1536 m), much lower than the snowline (1800–3200 m) . This sharp expansion event was also detected by BSP analyses after the LG for the overall population. However, BSP also indicated that S. nukiangensis in the current study strongly supports the previous hypothesis and was predicted by the feeding habits, hypognathous mouth and limited capacity for dispersal of S. nukiangensis. Geographic distances could be a reasonable explanation for the observed geographic distribution of genetic variation between populations. S. nukiangensis mainly preys on algae attached to stones  Moritz . Dam con


Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.DOI:http://dx.doi.org/10.7554/eLife.15266.001 Our genomes contain a record of historical events. This is because when groups of people are separated for generations, the DNA sequence in the two groups’ genomes will change in different ways. Looking at the differences in the genomes of people from the same population can help researchers to understand and reconstruct the historical interactions that brought their ancestors together. The mixing of two populations that were previously separate is known as admixture.Africa as a continent has few written records of its history. This means that it is somewhat unknown which important movements of people in the past generated the populations found in modern-day Africa. Busby et al. have now attempted to use DNA to look into this and reconstruct the last 4000 years of genetic history in African populations.As has been shown in other regions of the world, the new analysis showed that all African populations are the result of historical admixture events. However, Busby et al. could characterize these events to unprecedented level of detail. For example, multiple ethnic groups from The Gambia and Mali all show signs of sharing the same set of ancestors from West Africa, Europe and Asia who mixed around 2000 years ago. Evidence of a migration of people from Central West Africa, known as the Bantu expansion, could also be detected, and was shown to carry genes to the south and east. An important next step will be to now look at the consequences of the observed gene-flow, and ask if it has contributed to spreading beneficial, or detrimental, mutations around Africa.DOI:http://dx.doi.org/10.7554/eLife.15266.002 Advances in DNA analysis technology and the drive to understand the genetic basis of human phenotypes has led to a rapid growth in the amount of genomic data that is available for analysis. Whilst tens of thousands of genetic variants have been associated with different diseases in populations of European descent , less prAdmixture occurs when genetically differentiated ancestral groups come together and mix, a process which is increasingly regarded as a common feature of human populations across the globe . Genome-t Africa . Comparit Africa , provideWithin this timescale, the major demographic change within Africa was the transition from hunting and gathering to pastoralist and agricultural lifestyles . This shThe AGVP also found evidence of widespread hunter-gatherer ancestry in African populations, including ancient (9 ky) Khoesan ancestry in the Igbo from Nigeria, and more recent hunter-gatherer ancestry in eastern (2.5–4.5 ky) and southern (0.9–4 ky) African populations . The ideHere we analyse genome-wide data from 12 Eurasian and 46 sub-Saharan African groups. Half (23) of the African groups represent subsets of samples collected from nine countries as part of the MalariaGEN consortium. Details on the recruitment of samples in relation to studying malaria genetics are published elsewhere ; 2015. Tcoancestry), rather than independent markers, can provide a rich description of ancestral relationships and population history , to estTRUCTURE  to groupTRUCTURE . The paiTRUCTURE , and theTRUCTURE .The fineSTRUCTURE analysis identified 154 clusters of individuals, grouped on the basis of copying vector similarity . Some etancestry regions , estima expansion was accompanied by people is an active research question”. This is true: we cite recent research on the genetics of the Bantu expansion published within the last two years by Li et al. (2014) and Gonzales-Santos et al. (2015), as well as other work published with the last 15 years. We do not mean this to imply that there is an “ongoing controversy”, but see how it could have been read that way. We do think that it is a subject that has not been extensively studied with autosomal data, and in particular not using the latest admixture inference techniques. However, to address the reviewer’s concerns, we have rephrased this sentence and moved it to the Introduction:“The extent to which this cultural expansion was accompanied by people is an active research question, but an increasing number of molecular studies indicate that the expansion of languages was accompanied by the diffusion of people .”A separate issue is whether the Tishkoff et al. (2009) analysis “convincingly” demonstrated that the Bantu expansion involved a spread of West Africa people. Tishkoff et al. (2009) used autosomal microsatellite data, analysed with the STRUCTURE clustering algorithm and TESS , to demonstrate the presence of a geographically widespread cluster from Western to Southern Africa. They present results from various iterations of the STRUCTURE algorithm where they alter the value of K, the prescribed number of ancestral groups. This analysis shows that there is shared ancestry across much of sub-Saharan Africa, but doesn’t explicitly test whether this is the result of the Bantu expansion  do attempt with the same dataset). Moreover, as stated in the original STRUCTURE paper , “clusters may not correspond to real populations”, so it is not possible to say, from this analysis alone, that the observed patterns are the result of the Bantu expansion. In the current manuscript, we hope to have added to the debate by providing a fuller characterisation of the sources and timings of admixture involving “Bantu-like” groups at archaeologically acceptable dates. (See next comment.)5) In the second paragraph of the subsection “Population movements within Africa and the Bantu expansion”. The descriptions of the two linguistic hypotheses are particularly lacking in detail. It is important to put dates on the possible early and late splits, since the magnitude of the difference between these will determine the power to detect a difference genetically. Also, it is stated that recent genetic and linguistic analyses support the late split, but no mention of how. This is important for contextualising how this analysis adds to these other findings.We agree that more description is needed here, and specifically welcome the suggestion that we should include dates to the dispersals. We hope that the revision of this section better characterises the competing hypotheses , and we have tried to clearly lay out the arguments for the two hypotheses.6) In the third paragraph of the subsection “Population movements within Africa and the Bantu expansion”. I do not understand the logic behind the claim that the early split hypothesis predicts all of the ancestry of Eastern NC speakers comes from Central West Africa. The general consensus is that the Bantu expansion originated in the area of Cameroon or Nigeria ~5kya, then split into two major forks . The first spread around the Congo forest to the North, and entered East Africa in the Great Lakes region and continued down the eastern margin of Africa to Southern Africa. The second went around the Congo Forest down the Western Coast and entered Southern Africa. These two branches are thought to have ultimately reunited in Southern Africa. The analysis presented here finding Southern African NC ancestry in East African NC speakers might best be explained by the former descending from the latter. The ability to detect ancestry from western branch of the Bantu expansion is not possible here because there are no populations sampled from the area of Gabon, Angola, etc. I am worried these findings are a sampling artefact.If (as acknowledged by the reviewers) we can assume that our Cameroon populations  represent the best proxy for the ancestral Bantus, then we can use this to test the two split hypotheses. If East African NC speakers were the result of an early eastward migration across the top of the equatorial forests, then we’d expect to observe an old signal of admixture involving Cameroon surrogates in the admixture sources of these groups. If East African NC speakers were the result of a later split from the western Bantu instead, then we’d expect them to be more closely related to contemporary groups close this split, i.e. from south central Africa. To describe this more concisely, we now write:“The current dataset does not cover all of Africa. In particular, it contains no hunter-gather groups outside of southern Africa, and no representation of the western Bantu except the Herero from Namibia. […] We note that these may change with future analyses involving populations from the relatively under-sampled central southern Africa.”What we observe in East Africa NC speakers are events involving a major source containing surrogates most similar to Malawi  In the subsection “(3) Medieval contact between Asia and the East African Swahili Coast”. Again it is not clear that this represents the Western Bantu expansion since the samples come from Cameroon which is hypothesised to be near the homeland of both the Eastern and Western branches of the expansion.We hope that we have provided sufficient additional detail and caveats in the section re-write, and in answer to comment  above to8) In the subsection “(7) Pre-Bantu pastoralist movements from East to South Africa”. The proposed model here is incongruent with the known archaeology, which shows the Bantu expansion reaching the eastern side of the Congo Forest in the north near Lake Victoria, rather than the south. The archaeology may not be correct, however given the lack of western Bantu samples included in this study, the conservative interpretation is that these findings are a sampling artefact.As we have hopefully described more fully in the revised manuscript, the model that the reviewer suggests, of an early expansion to eastern Africa north of the Congo forest to Lake Victoria, is referred to as the early-split hypothesis. We believe our analysis, in addition to other recent genetic  and linguistic  work is more consistent with the late-split hypothesis. We wrote at the beginning of this subsection (“A haplotype-based model of gene-flow in sub-Saharan Africa”) that “Using genetics to infer historical demography will always depend on the available samples and population genetics methods used to infer population relationships.” We therefore hope that we have outlined the relevant caveats for our model of gene-flow events in both this section, and the previous one, regarding the Bantu expansion.9) In the first paragraph of the Discussion. The adoption of pastoralism began well before 2,000 years ago. The earliest archaeological evidence of cattle keeping may date to as early as 9kya in the Nile River Valley, and is well established by 6kya . Pastoralists reach the Koobi Fora region of Kenya by 4.5 kya, and are east of Lake Victoria by 3.8 kyat (see Pendergast 2011).Thank you for this comment. We have altered this sentence to read:“An unanswered question in African history is how contemporary populations relate to those present in Africa before the transition to pastoralism that began some 9kya.”10) In the first paragraph of the Discussion. Why is the GLOBETROTTER analysis more precise? Is there any evidence to support the assertion? Also, even if more precise, is it more accurate?This is a statement about how well the sources of admixture are characterised by the two admixture inference approaches. In The precision of GLOBETROTTER was tested against ROLLOF (an earlier incarnation of MALDER) in the original GLOBETROTTER paper  and found to provide date estimates with tighter confidence intervals on simulated data than ROLLOF. Accuracy was also assessed in that paper, with the confidence interval containing the true date in over 90% of ~5,000 simulated admixture scenarios.However, we note that precision has a particular scientific meaning, which has not been explicitly tested in the current setting. We therefore removed this sentence from the Discussion, and instead write:“The f3 and MALDER analyses show evidence for deep Eurasian and some hunter-gatherer ancestry across Africa, to which our GLOBETROTTER analysis  provides11) Methods section: The Methods section is often difficult to follow because it frequently mixes results with the methods themselves. If results of one analysis are necessary to inform how the following analysis is to be performed, it would be preferable to lay out the strict methods and the logic of how methodological options were chosen in the Methods section, and then keep the actual progression of results in the Results section.Thank you for this comment. We have edited the Methods section to keep to the suggested logical progression. In particular we:A) Integrated the first paragraph of section 2.4 describing the fineSTRUCTURE results to the Results section;B) Removed the description of the MALDER curve amplitude analysis from section 3.1;C) We renamed Section 3.5 and moved text to the figure supplement legends;D) We renamed Section 3.6;E) We moved the section (3.15) titled “Summary of inferred gene-flow from West to East and South Africa” to a new 12) More generally, the manuscript is a bit too long; in particular, the Discussion and Abstract contain a substantial amount of content on genetic epidemiology and infectious disease that is only tangentially related to the analyses performed in the manuscript.We have chosen to provide context to our analysis, both in relation to previous work by using similar admixture inference methods to previous authors together with our “new” haplotype-based analyses of African genetic variation, but also by discussing more generally how results such as ours should be interpreted , as well as the relevance of this work to the wider field (“Admixture and genetic epidemiology”).eLife by providing minimal supplementary information with the manuscript and putting all of our content into the main manuscript, which, in addition to the description and discussion of the multiple different analyses has led to a long paper.We have made an effort to trim the manuscript to improve clarity whilst hopefully retaining important context and caveats (particularly the Introduction and Discussion). We have tried to keep to the ethos of 13) The description of the TVD analyses  could be clarified. The comparison of TVD vs. Fst suggests that TVD is more informative ("expected to capture more variability") because recombination rates are faster than mutation rates. However, aren't recombination rates and mutation rates quite similar (both roughly 10^-8 per base per generation)? Also, the difference between TVD and Fst seems to be more than just amount of information captured; the two metrics must be capturing different types of information given the empirical differences between the values of the metrics. More intuition would help. Overall, I found the discussion of TVD rather confusing, especially given that paragraph ends with a caveat about interpretation – what then should we make of the TVD results in F_ST and TVD are both metrics that allow one to generate a single value that represents the genetic difference between two populations. Whilst F_ST is based on the variance in allele frequencies between populations, TVD is measures the absolute differences in copying between two populations by comparing their copying vectors. The reviewer is right to say that they are capturing different types of information: F_ST is a measure of how drifted two populations have become, whereas TVD attempts to measure shared ancestry directly. Another way of thinking about it is that TVD reflects similarities across sets of contiguous SNPs, or haplotypes, whereas F_ST looks at each allele independently. We have rephrased the section on TVD to better describe the metric and the intuition about what it can tell us.We have also added an additional figure  where we14) In the main GLOBETROTTER analyses, the authors note that the GLOBETROTTER approach allows them to infer whether Eurasian haplotypes came directly into sub-Saharan Africa or were brought indirectly together with sub-Saharan groups . Is this statement technically correct? It seems to me that inference of this sort would require looking for colocation of Eurasian + other sub-Saharan haplotypes . Such a signal would indeed be strong evidence of Eurasian haplotypes entering via a previous admixture, but as far as I can tell GLOBETROTTER only looks at copying vectors (vs. relative locations of copied segments).This statement is based on the idea that GLOBETROTTER can reconstruct the genetic composition of admixture sources as mixtures themselves. GLOBETROTTER does this by identifying whether ancestry chunks from two different populations (as inferred through chromosome painting) tend to be situated at close genetic distances, in which case ancestry from both populations will have arrived together, or whether these ancestry chunks tend not to be associated with each other, in which case they likely arrived from different admixture source inputs. We use the painted chromosomes to look at the distribution of these ancestry chunks, and so the mixtures in these source groups are indeed based, in some sense, on the co-localisation of ancestry in the genome. The source group composition is thus informative of the identity of the admixture sources, so when we observe an admixture source which is almost exclusively Eurasian, then this does imply that the admixture source (given the available surrogates used) was likely to have been mostly Eurasian.