of Montagu’s harriers. Such a relaxed philopatric beha- vior has indeed been described for the species .
Our results strongly support a recent population expan- sion as an important cause of the relative homogeneity across populations. Such expansion is indicated by the shallow phylogenetic tree and by the star-like haplotype network (Figure 2). The genetic signature observed in the two main Montagu ’s harrier groups of populations (SW vs. NE) is consistent with the occurrence of post- glacial demographic expansions during the second half of the Holocene, as evidenced by the BSP analyses. These revealed two events of population growth that occurred first in the SW (ca. 7500-5500 years BP), and later in the NE part of the range (ca. 3500 to 1000 years BP; Figure 3). The effective population size increases also appeared more pronounced in the NE than in the SW populations (Figure 3). Furthermore, these two groups of populations diverged around 5200 years ago, between the two waves of population growth. This pat- tern may be explained by regional differences in the impact of both climate changes and human activity on vegetation during the Holocene. Ample evidence sup- port that during the last glacial maximum (37,000- 16,000 years BP), the tundra-steppe vegetation was widespread from France to the Bering strait (e.g. ). Therefore, according to the preference of Montagu’s harrier for open steppe-like landscapes, the species would have been widely distributed throughout Eurasia. Then, during the following interglacial period at the beginning of the Holocene, about 10,000 years ago, this vast system disappeared almost completely as a conse- quence of the quick expansion of temperate forests (in Europe) and taigas (in Asia) from their ice-Age refugia . This probably led to strong range contraction and population declines in steppe-associated communities. Unfortunately, based on our data set, coalescent times go back only 10,000 years, therefore changes in popula- tion size before that date (e.g. after the last glacial maxi- mum ca.18,000 to 10,000 years BP) cannot be inferred.
thereby contributing to greater geneflow.
Mark-recapture studies and genetic analyses of foundress associations have shown that cooperating wasps tend to be philopatric and preferentially join former nestmates, with an average relatedness r > 0.6 [4, 18, 31]. In a study of P. fuscatus nesting behavior, Klahn found that individuals within larger foundress associations tended to be located closer to their natal nest sites, when compared to their less cooperative counterparts . In spite of the evidence for natal philopatry in cooperative species, the relationship between cooperation and population structure in Polistes wasps is contentious. Lengronne et al. found similar degrees of fine-scale geneticstructure in populations of P. canadensis and P. dominula, which vary significantly in their rates and degrees of cooperative founding . Even species of Polistes that are exclusively solitary-founding can show high degrees of female philopatry [23, 38]. Thus, the relationship between cooperation and dispersal in Polistes is unknown and requires further study.
Conclusion: The demographic pattern suggests that An. pseudopunctipennis has undergone a single colonization process, and the ancestral haplotype is shared by specimens from all localities, indicating mitochondrial geneflow. Genetic differentiation was minimal, observed only between one northern and one southern locality. The estimated time of the population expansion of this species was during the Holocene. These data suggest that regional vector control measures would be equally effective in both northern and southern localities sampled, but also that insecticide resistant genes may spread rapidly within this region.
same cluster. This distance matrix was then used to build a dendrogram for all 282 samples. The number k of final clusters (conserved groups) was selected based on the dendrogram structure (Additional file 5B). The value for k = 9, 10 and 14 were producing relevant clusters, but on comparing the barcodes with the previously defined population structure , it was observed that the clusters produced on increasing k after 9 are not associated to a specific resistant population (KH2, KH3 and KH4) and instead are related to admixed population KHA and the mixture of other resistant subpopulations. These unspe- cific clusters were localized close to centre of the coun- try. Hence, the population structure was represented by nine conserved groups (G1 to G9). Weblogo was used to highlight conserved alleles among health centres in G1 to G9 groups. The groups are geolocalized by the geo- graphical centroids on the 2D map. The coordinates for the geographical centroids are calculated as the average of the coordinates (measured in the coordinate space of the 2D map) of the health centres included in the group. To determine the groups significantly related to geo- graphical locations, the average distance to geographical centroid within a group was compared to the average dis- tance to the geographical centroid when the 282 samples were randomly assigned to the nine groups. The average distance for each group was compared to the average
create genealogies for unrecombined genomic segments. Re- combination graphs can provide greater power for detecting demographic effects with fewer samples, although it can be more computationally demanding to run relevant analyses (Schiffels and Durbin 2014). Adding recombination will prove important for facultative sexual coalescents because while sex has to be very rare [Oð1=NÞ] to affect the nonre- combining genealogies presented here, differences in recom- bination graphs might become apparent with higher rates of sex. This is so because it is expected that recombination cor- relates linearly with sex rate. A similar result was derived for partially selﬁng organisms by Nordborg (2000). Genomic sequences of facultative sexual organisms can reveal evi- dence of rare recombination events, providing proof of cryp- tic sex [examples were shown by Grimsley et al. (2010) for the marine algae Ostreococcus spp. and Signorovitch et al. (2005) for Placozoa]. In addition, ancestral graphs would be able to separate out areas of the genome affected by gene conversion, leading to much more reﬁned measurements of how this force affects genetic architecture. In particular, gene conversion events in the absence of sex will lead to much higher rates of gene conversion relative to crossing over. This will have a strong effect on short- vs. long-range linkage dis- equilibrium along chromosomes, which may enable accurate estimators of the rate of sex even in the presence of signiﬁcant rates of gene conversion. Recombination graphs of facultative sexual organisms thus can greatly increase the power by which the effects of infrequent sex and demography can be disentangled.
A few lessons may benefit future studies of German cockroach dispersal and differentiation. It would be beneficial to use markers which are sufficiently variable to detect intra-specific variation but less subject to the drift and non-equilibrium conditions that are likely to affect German cockroach populations. If microsatellites are to be used, a greater number of loci may be required to overcome the loss of diversity from these conditions. Gene sequencing may be the preferred option since it captures the highest possible resolution of genetic variation with no bias (Schlötterer 2004). It is unclear whether mtDNA will be a feasible option, since only 10 haplotypes were found across our 40 global populations. There may prove to be too little variation in the mitochondrial genome of B. germanica to investigate levels of geneflow and differentiation. The challenge will be to find a nuclear or mitochondrial gene which has enough variation for population-level analysis but does not require so many sequences to be obtained per population so as to be prohibitively expensive.
The work on population structure of F. thapsinum from Kansas, Africa, Thailand, and Australia, found that migration with seeds brought from different parts of the world and random mating in situ probably are important in determining the population structure of this fungal pa- thogen. In an extensive study of F. thapsinum from Australia similar conclusions were reached, i.e., that the Australian population of F. thapsinum is part of an international panmictic popula- tion of this species (Petrovic, 2007). Large collections of F. thapsinum from, e.g., India and east- ern, western and southern Africa, where sorghum has been domesticated and commercial sorg- hum breeding programs have a long history, are needed to determine that additional center(s) of diversity exist and to evaluate the genetic relationships observed within and between the popula- tions evaluated to date.
between animal species are rare, but may also stem from a belief that hybridization and introgression between spe- cies is unnatural [1,3,5]. Hybrids are usually rare on a per individual basis, but species undergoing occasional inter- pecific hybridization are common. Existing surveys sug- gest that around 10% of animal species, and 25% of plant species hybridize : for instance, 9% of bird species  and 11% of European butterfly species  are known to hybridize with at least one other species. Even if occa- sional, natural hybridization can lead to successful intro- gression, with important consequences in ecology, evolution and conservation [3,5]. However, hybridization in nature does not guarantee that genes will pass between species, because hybrids are typically selected against, and may be completely infertile or inviable. To determine whether hybridization leads to introgression, we must investigate the patterns of distribution of alleles among hybridizing species. Shared alleles in descendent species may have been inherited as pre-existing polymorphisms from their joint ancestors, as well as via recent geneflow since speciation. These two routes to allelic sharing, which both result in genealogical polyphyly at the species level, are hard to distinguish on the basis of genetic data. Recently, two classes of molecular methods have been used to test for introgression. Both rely on the idea that introgression in some genomic locations will be prohib- ited by reproductive isolation or divergent natural selec- tion, while at other loci introgressing alleles will establish more freely. In fact, without heterogeneity of divergence across the genome, it will typically be difficult to discrim- inate recent speciation from recent geneflow. The first method examines genotypic data at multiple low-resolu- tion loci, such as chromosomal morphs, allozymes, mic- rosatellites, amplified fragment length polymorphisms (AFLPs) or single nucleotide polymorphisms (SNPs), for heterogeneity of divergence in allele frequency. Alleles that flow freely will have their frequencies homogenised across species, while alleles whose introgression is blocked by divergent selection will retain strong frequency differences. Thus, heterogeneity in allele frequency differ- ences among loci suggests that on-going geneflow as a likely explanation for similar allele frequencies at some genes in pairs of taxa that hybridise [8-13]. A second approach, adopted in this paper, employs DNA sequence data, coupled with a statistical approach based on gene genealogies and coalescence theory, to test whether shared haplotype polymorphisms could have been inher- ited from a common ancestor or are more likely due to introgression since speciation [14-18].
To address the genetic isolation of Key deer in hypothesis one, I edited cytb sequences in Sequencher v5.1 (Gene Codes Inc., Ann Arbor, MI, USA) and aligned the data in MEGA6 (Tamura et al. 2013) using ClustalW. I first created a TCS network (Clement et al. 2000) using popART (http://popart.otago.ac.nz) to find unique haplotypes. Next, I determined the highest likelihood models of evolution for my cytb data and evaluated partitioning of the gene based on codon position using PartitionFinder v1.1.1 (Lanfear et al. 2012). I constructed a Bayesian phylogeny utilizing MrBayes v3.2.2 (Ronquist et al. 2012) and partitioned my data by first, second and third codon positions. Each partition was run under a separate model: HKY+G, K80+I, and HKY, respectively (see Results). I ran MrBayes with only unique haplotypes identified from TCS and with two independent runs of 5×10 6 generations and the first 10,000 trees were discarded as burn-in to generate the phylogeny. To evaluate mitochondrial diversity in terms of nucleotide and haplotype diversity, I used the program DnaSP v5.0 (Librado & Rozas 2009).
Advances in the knowledge-base of African freshwater fisheries have been made over the last five decades [1–3]. Like elsewhere in the world, these advances in knowledge have been driven mainly by threats that are facing the sustainable exploitation of fisheries resources. For African fisheries, these threats include increases in urbanisation linked to human population growth, exotic fish introductions, overfishing, and sedimentation / pollution as a result of changes in land utilisation. The impacts of these threats are particularly noticeable in the freshwater lake basins of East Africa [3–5]. Most freshwater fish research has focused on the evolution of one group of African fishes, the haplochromine cichlids (Cichlidae) in the Great Lakes region. Sev- eral mutually contradictory reports have characterised the haplochromine cichlids’ high level of endemism and population demise as a result of human-induced impacts [6–10]. However, many other African species remain data deficient in the face of declining fisheries. This poses a serious threat to the economic development of African communities that largely depend on fish in these lakes and rivers for their livelihoods [11–13].
the population tends to reduce national household saving. Second, in a developing country without a mature social security system, the older population have to rely on the support (long-term care) from their children. Thus children act as an effective substitute for life-cycle saving. (Choukhmane et al. (2014), He et al. (2016), Imrohoroğlu and Zhao (2018b)). In addition, Modigliani and Cao (2004) use the share of the employed population out of the number of minors up to age 15 to approximate demographic change. They find that the decline in the young population dependency between 1953 and 2000 increased Chinese household saving through both effects of “fewer mouths to feed” and old-age security. However, this time series evidence is not confirmed by panel data studies. Neither aggregate dependency ratio (Kraay (2000)) nor separate accounts of the young and the old dependency ratios (Horioka and Wan (2007)) are found to have a significant effect on the household saving rates across Chinese provinces. Applying cohort analysis to data from the Urban Household Survey (UHS), Chamon and Prasad (2010) reach a similar conclusion that demographic structural shifts do not go very far in explaining saving behavior in China. Wei and Zhang (2011) consider the saving motive from the perspective of the sex ratio. They find that Chinese parents with a son competitively raise their savings to improve their son’s relative attractiveness for marriage and the pressure on savings spills over to other households. However, they may omit the saving motives in preparing for the education and life expenditure of children as the children grow up. Specifically, this refers to the difference in the expenditure of raising boys and girls which is originated from the traditional culture “Poor Boys, Rich Girls.”
based methods may not easily distinguish between recent immigrants that reach sexual maturity and reproduce (and contribute to geneflow) and those that do not.
With the recent incorporation of individual-based approaches into the genetic toolkit of 113
Nonmonophyletic gene trees are common in empirical studies of well-established species (Carling and Brumfield 2008; Carstens and Dewey 2010; Lee et al. 2012). The large effective population size of nuclear genes and thus the large effect of ILS make it less likely that any single nuclear gene will recover the true species tree (Knowles and Carstens 2007). As a result, species tree estimation using multiple nuclear loci is quickly replacing single locus studies as a best practice in phylogenetics (Brito and Edwards 2009; Degnan and Rosenberg 2009) and species delimitation (Yang and Rannala 2010; Ence and Carstens 2011). The influence of ILS on phylogeny estimation has been studied quite extensively (Degnan and Salter 2005; Degnan and Rosenberg 2006; Maddison and Knowles 2006); however, the effect of geneflow on species tree inference has received far less attention. We have referred to the units of our simulations as species, but under some simulation conditions (i.e., high migration rates) they are probably more accurately described as populations belonging to the same species. However, empiricists often find themselves in the quandary of not knowing whether the units of analysis are populations or species. Thus, the results of our simulations are relevant to phylogeographic and species
A more defined population structure was expected in the agricultural compared with the natural area because of habitat fragmentation. From the geneticstructure analysis it was shown that the three main areas and the most distant field in the Fussingø area formed four separate clusters as expected given the low dispersal ability of this species (Sandell et al., 1991; Figure 2). More interestingly, separate genetic clusters were present in the agricultural areas but not in the natural one, and the presence of the same isolated populations within the two agricultural areas were confirmed by all analyses (Figure 2). However, given that this observation was based on only one natural area it should be interpreted cautiously. In particular, n the Fussingø area, this clustering was evident also from cytochrome-b data where the haplotype distribution mirrored the geneticstructure recovered by the STRUCTURE analysis (Figure 2 and Supplementary Information,
Moose reproduction was maximal in the steppe zone of Ukraine during the period of its highest population (1981-1990, Таble 3); however, during expansion and dispersion the population essentially declined. Possibly, this was related to the dominance of young females in the population that are less fertile than ani- mals of middle age (Filonov 1983). The mean calving rate was 1.3 ± 0.10/pregnant or 0.4/ adult female (Volokh 2002). On average there were 78% singletons, 25% twins, and 3% trip- lets; however, the adult reproductive rate was only 39%. In comparison, this rate was 46% north of and 69% south of the forest zone in Russia, with1.2-1.4 embryos/pregnant female and 0.6-1.1 embryos/adult female (Filonov 1983). An analysis of 27,300 licenses from harvested females indicated embryo/adult female ratios of 1.2-1.4 in European Russia and 1.3 in the forest-steppe and steppe zones. In the latter case, the proportion of pregnant females to adults was 0.3-0.8 (Rozhkov et al. 2001), which was similar to the fertility rate of moose at their southern range in the steppe region of Ukraine. It is interesting that repro- ductive rates were 80-100% along the northern border of moose range in Finland (Rajakoski and Koivisto 1970), and fertility fluctuated from 0.3 for young animals to 1.1 for animals of middle age (Nygren et al. 1999).
mechanisms are of key interest in the understanding of the colonization abilities of plants at the landscape scale (Verhagen et al. 2001; Pywell et al. 2002). During last two decades, an increasing number of attempts have been undertaken to get reliable knowledge of which plants are dispersed zoochorously and which factors and plant traits direct zoochorous dispersal (Cosyns et al. 2005 ). There are now many studies which have quantified such effects on a wide range of plants and habitats, such studies, are still very limited in semi-steppe rangelands (Jaroszewicz et al 2009). Steppe and semi-steppe rangeland systems are structurally diverse, exhibiting differences in woody plant canopy cover, stature, shrub functional form (evergreen vs. deciduous; broad-leaved vs. needle-leaved vs. succulent-leaved; shallow vs. deeply rooted), grass functional form[annual vs. perennial, C3 vs. C4 photosynthetic pathway] and spatial arrangement [random, regular, or clumped trees, bunch vs. rhizomatous grass] (Archer et al. 2001). The effectiveness of endozoochory and germination success of plant species after passage through the animal gut is a function of quantitative and qualitative traits. The quantity of dispersal depends on the amount of seeds ingested, animal type and livestock digestive system (Herrera and Jordano 1981). This can happen either deliberately due to high palatability or accidentally when a herbivore consumes seeds along with palatable leaves or neighboring palatable plants (Janzen, 1984; Pakeman et al., 2002). While the quality of dispersal depends on the percentage of undamaged seeds that are defecated. Germination may be enhanced by the softening of the coats during the digestive process, but destruction of seeds or inhibition of germination can also occur (Ramos et al. 2006). Some seeds adapted for endozoochory require scarification, the abrasion or chemical degradation of the seed coat that may be required by some species in order for the seeds to germinate (Davise 2007). Deposition of seeds with fecal material may provide nutrients that promote seedling establishment, but seed germination and seedling establishment could also be inhibited due to the toxicity and hydrophobic nature of dung (Ramos et al. 2006). Additionally, Seed germination successes after gut passage are not simply a function of the parent plant. Animal species have different effects on seed germination because of the differences in the oretical mean retention times of digestive products (Wallander et al. 1995; Mueller et al. 1998).
2007. In these cases, where the population might have been structured, the calculation of N e should be based on the paired increase of coancestry (N e C jk ) (Cervantes et al. 2011; Leroy et al. 2013). The effec- tive population size based on individual increase in inbreeding (N e F i ) considers all historical pedigree information, and thus is affected by possible popula- tion structures. Nonetheless, computation through both methods is useful because they can provide different information, and the comparison between both values can inform on the degree of population structuring (Cervantes et al. 2011). In this study, the N e C ij for the reference populations were 54.66 and 62.08 in AlivePop and AliveBpop, respectively. Dif- ferently, the N e F i ranged from 21.64 and 24.84 for AlivePop and AliveBpop, respectively. While the first estimates stood above the international rec- ommendations by FAO, which is 50 to maintaining genetic variability in conservation and breeding programmes, the individual inbreeding-based values were considerably below. The difference between both calculated population sizes is considerable, and the N e C jk /N e F i ratio significantly differs from one which would be expected in an ideal popula- tion. This fact suggests diffuse structuring within the population that might have been originated by preferred matings.
adaptation. Consequently the outcome of climate change, on top of other environmental constraints (e.g. presence of water and Monte vegetation, occurrence of cliffs), could be particularly important for some of the populations, in particular the currently endangered Bloxami and Andinus populations. Under added selec- tion pressure, such as that imposed by ongoing climate change, populations can respond in roughly three ways: 1) by shifting in abundance and distribution, 2) by going extinct, or 3) by evolving . Even if predicting which one, or even which combinations of them, will occur is difficult [92,93], some likely scenarios can be expected for the burrowing parrot population clusters. Shifts in the distribution could be possible in the case of Bloxami, distributed in Chile. Due to intensive poaching, several cliffs along the historical distribution of the species (Fig- ure 1), which traditional contained colonies, have been found to be empty at present [41,85] (JFM pers. observ.). Provided that water and natural food items are still available in those places, and that the current small size of Bloxami is not further reduced, these colonies could be reoccupied by burrowing parrots. The situation appears to be quite different for the size-reduced Andi- nus population in the Cuyo region of Argentina (Addi- tional file 4 Figure S1). In this area, only few suitable breeding places (high cliffs close to water and Monte vegetation) are available, leaving this population only two possibilities in case of strong or too sudden climate change: going extinct or evolving. For Patagonus1 and Patagonus2, two genetically distinct, yet phenotypically indistinguishable populations, the situation appears to differ again. In a few occasions, individuals from several colonies of these populations were found to breed in nests dug in human-build structures like shafts of mines, abandoned adobe buildings and wells for collect- ing water for cattle . Additionally, some suitable breeding places are available in the southernmost as well in the easternmost areas of the historical distribu- tion of the species. Provided the future occurrence of a more benign climate in the South and a release of human-induced pressure in the East, some of those areas could be used by burrowing parrots. However, the currently rapid habitat degradation in the region inhab- ited by Patagonus1 and Patagonus2 (see above) makes this possibility very uncertain, as in fragmented land- scapes, rapid climate change has the potential to over- whelm the capacity for adaptation of the populations and dramatically alter their genetic composition . Altogether, how closely adaptation can be expected to accommodate climate change and the additional pres- sure of habitat loss and fragmentation, remains a ques- tion for further research.
1984). In contrast, despite frequent geographical contact between species from the series Piperitae and the series Obliquae (also subgenus Mono calyptus), there are only a few records of inter series hybrids (Pryor 1957a, Jackson 1958, Potts & Reid 1983). In the present study we compare the extent of inter-series and intra-series hybridisation and geneflow between two Piperitae species (E. pulchella Desf. and E. coccifera Hook. f.) and one Obliquae species (E. delegatensis R.T. Baker) at Snug Plains in southeastern Tasmania by examining the flowering phenology and adult and seedling morphology.