Jump dispersal drives the relationship between micro- and macroevolutionary dynamics in the Sicydiinae (Gobiiformes: Oxudercidae) of Sundaland and Wallacea.

Insular biodiversity hotspots of Southeast Asia are remarkable for their biodiverse faunas. With a marine larval phase lasting up to several months, the freshwater fish subfamily Sicydiinae has colonized most islands of these hotspots. However, Sicydiinae diversity is still poorly understood in Southeast Asia. With the objective to estimate intraspecific genetic diversity and infer past demography, we conducted the molecular inventory of Sicydiinae species in Sundaland and Wallacea using 652 bp of the mitochondrial cytochrome oxidase I gene, species delimitation methods and Bayesian Skyline plot reconstructions. In total, 24 Molecular Operational Taxonomic Units are delimited among the 603 sequences belonging to 27 species and five genera. Two cases of discordance between morphology and mitochondrial sequence are observed suggesting ongoing speciation and/or introgression in two genera. Multiple new occurrences are reported, either for a single biodiversity hotspot or both, some of which corresponding to observations of a few individuals far from the range distribution of their conspecifics. Among the ten species or species group whose intraspecific diversity was examined, high levels of genetic diversity and past population expansion are revealed by Tajima's D tests and Bayesian Skyline Plot reconstructions. Together these results indicate that long-distance dispersal is common and suggest that most endemic species originated through founder events followed by population expansion. Patterns of sexual dimorphism and males' coloration among diverging species pair seem to point to sexual selection as an important mechanism contributing to speciation in the Sicydiinae of Sundaland and Wallacea.

Genetic evidence for widespread population size expansion in North American boreal birds prior to the Last Glacial Maximum.

Pleistocene climate cycles are well documented to have shaped contemporary species distributions and genetic diversity. Northward range expansions in response to deglaciation following the Last Glacial Maximum (LGM; approximately 21 000 years ago) are surmised to have led to population size expansions in terrestrial taxa and changes in seasonal migratory behaviour. Recent findings, however, suggest that some northern temperate populations may have been more stable than expected through the LGM. We modelled the demographic history of 19 co-distributed boreal-breeding North American bird species from full mitochondrial gene sets and species-specific molecular rates. We used these demographic reconstructions to test how species with different migratory strategies were affected by glacial cycles. Our results suggest that effective population sizes increased in response to Pleistocene deglaciation earlier than the LGM, whereas genetic diversity was maintained throughout the LGM despite shifts in geographical range. We conclude that glacial cycles prior to the LGM have most strongly shaped contemporary genetic diversity in these species. We did not find a relationship between historic population dynamics and migratory strategy, contributing to growing evidence that major switches in migratory strategy during the LGM are unnecessary to explain contemporary migratory patterns.

Bayesian Skyline Plots disagree with range size changes based on Species Distribution Models for Holarctic birds.

During the Quaternary, large climate oscillations impacted the distribution and demography of species globally. Two approaches have played a major role in reconstructing changes through time: Bayesian Skyline Plots (BSPs), which reconstruct population fluctuations based on genetic data, and Species Distribution Models (SDMs), which allow us to back-cast the range occupied by a species based on its climatic preferences. In this paper, we contrast these two approaches by applying them to a large data set of 102 Holarctic bird species, for which both mitochondrial DNA sequences and distribution maps are available, to reconstruct their dynamics since the Last Glacial Maximum (LGM). Most species experienced an increase in effective population size (Ne , as estimated by BSPs) as well as an increase in geographical range (as reconstructed by SDMs) since the LGM; however, we found no correlation between the magnitude of changes in Ne and range size. The only clear signal we could detect was a later and greater increase in Ne for wetland birds compared to species that live in other habitats, a probable consequence of a delayed and more extensive increase in the extent of this habitat type after the LGM. The lack of correlation between SDM and BSP reconstructions could not be reconciled even when range shifts were considered. We suggest that this pattern might be linked to changes in population densities, which can be independent of range changes, and caution that interpreting either SDMs or BSPs independently is problematic and potentially misleading.

"Colonization routes and demographic history of Chirostoma humboldtianum in the central Mexican plateau".

In the present study we evaluate the population structure and potential colonization routes of the silverside Chirostoma humboldtianum through approximate Bayesian computations. Six microsatellite loci were amplified in a total of 288 individuals from six different locations covering the complete geographic distribution of the species. Additionally, two mitochondrial DNA markers, a D loop control region and cytochrome b were amplified in a subset of 107 individuals. The results found with microsatellites allow recovering well-structured populations that have experienced a drastic reduction in the effective population size. On the other hand, mtDNA sequences showed a moderate phylogeographic structure with shared haplotypes between geographic localities and signalsof a slight increase in the effective population size. Finally, the approximate Bayesian computation analysis performed with both datasets suggested a west-to-east colonization route for the species in Central Mexico.

Range-wide genetic structure and demographic history in the bat ectoparasite Cimex adjunctus.

BACKGROUND: Evolutionary histories of parasite and host populations are intimately linked such that their spatial genetic structures may be correlated. While these processes have been relatively well studied in specialist parasites and their hosts, less is known about the ecological and evolutionary consequences of relationships between generalist ectoparasites and their hosts. The aim of this study was to investigate the genetic structure and demographic history of a bat ectoparasite, Cimex adjunctus, whose host affinity is weak but the biology of the potential hosts have been well studied. This ectoparasite has been hypothesized to rely on its hosts for dispersal due to its low inherent dispersal potential. Here we describe genetic diversity and demographic history in C. adjunctus through most of its range in North America. We investigated variation at the cytochrome c oxidase 1 mitochondrial gene and nine microsatellite markers, and tested the prediction that genetic diversity in C. adjunctus is spatially structured. We also tested the prediction that demographic history in C. adjunctus is characterized by range and demographic expansion as a consequence of post-Pleistocene climate warming. RESULTS: We found stronger spatial structuring of genetic diversity in C. adjunctus than has been quantified in two of its hosts, but contrast in amount of variation explained by host association with different genetic markers (i.e., nuclear vs mitochondrial DNA). Also, C. adjunctus' history is not primarily characterized by demographic and range expansion, as is the case with two of its key hosts. CONCLUSIONS: Our study shows different patterns of genetic structure and demographic history in C. adjunctus than have been detected in two of its key hosts. Our results suggest an effect of a loose parasite-host relationship and anti-parasitism strategies on genetic structure and post-Pleistocene recovery of population size.

Contrasting responses to a climate regime change by sympatric, ice-dependent predators.

BACKGROUND: Models that predict changes in the abundance and distribution of fauna under future climate change scenarios often assume that ecological niche and habitat availability are the major determinants of species' responses to climate change. However, individual species may have very different capacities to adapt to environmental change, as determined by intrinsic factors such as their dispersal ability, genetic diversity, generation time and rate of evolution. These intrinsic factors are usually excluded from forecasts of species' abundance and distribution changes. We aimed to determine the importance of these factors by comparing the impact of the most recent climate regime change, the late Pleistocene glacial-interglacial transition, on two sympatric, ice-dependent meso-predators, the emperor penguin (Aptenodytes forsteri) and Weddell seal (Leptonychotes weddellii). METHODS: We reconstructed the population trend of emperor penguins and Weddell seals in East Antarctica over the past 75,000 years using mitochondrial DNA sequences and an extended Bayesian skyline plot method. We also assessed patterns of contemporary population structure and genetic diversity. RESULTS: Despite their overlapping distributions and shared dependence on sea ice, our genetic data revealed very different responses to climate warming between these species. The emperor penguin population grew rapidly following the glacial-interglacial transition, but the size of the Weddell seal population did not change. The expansion of emperor penguin numbers during the warm Holocene may have been facilitated by their higher dispersal ability and gene flow among colonies, and fine-scale differences in preferred foraging locations. CONCLUSIONS: The vastly different climate change responses of two sympatric ice-dependent predators suggests that differing adaptive capacities and/or fine-scale niche differences can play a major role in species' climate change responses, and that adaptive capacity should be considered alongside niche and distribution in future species forecasts.

Patterns of species range evolution in Indo-Pacific reef assemblages reveal the Coral Triangle as a net source of transoceanic diversity.

The Coral Triangle in the Indo-Pacific is a region renowned for exceptional marine biodiversity. The area could have acted as a 'centre of origin' where speciation has been prolific or a 'centre of survival' by providing refuge during major environmental shifts such as sea-level changes. The region could also have acted as a 'centre of accumulation' for species with origins outside of the Coral Triangle, owing to it being at a central position between the Indian and Pacific oceans. Here, we investigated support for these hypotheses using population-level DNA sequence-based reconstructions of the range evolution of 45 species (314 populations) of Indo-Pacific reef-associated organisms. Our results show that populations undergoing the most ancient establishment were significantly more likely to be closer to the centre of the Coral Triangle than to peripheral locations. The data are consistent with the Coral Triangle being a net source of coral-reef biodiversity for the Indo-Pacific region, suggesting that the region has acted primarily as a centre of survival, a centre of origin or both. These results provide evidence of how a key location can influence the large-scale distributions of biodiversity over evolutionary timescales.

Rethinking refugia: Tree topology, divergence dates, and demographic history trace the distribution of the endangered Plymouth gentian (Sabatia kennedyana) from the Pleistocene glaciation to present day.

PREMISE OF STUDY: Molecular population genetics is a powerful tool to infer how species responded to past environmental change. In the northern hemisphere, interest is increasing in how species responded to changes in ice coverage and temperature during the last glaciation maximum (LGM, between 18000-21000 yr ago) with a common assumption that glacial refugia were located at the southern edge of a species range. METHODS: We reconstructed the glacial and postglacial phylogeography of Sabatia kennedyana, a member of the Atlantic Coastal Plains Flora with a current distribution from Nova Scotia (NS) to South Carolina, using both cpDNA and nuclear markers. We also examined clinal variation in morphological traits, in particular relative investment in asexual vs sexual growth. KEY RESULTS: We find strong evidence that the species did not reside in southern glacial refugia, but rather in primary glacial refugia off the exposed continental shelf extending from Cape Cod and that this area was responsible for the founding of modern populations across the range from Nova Scotia (NS) to the United States. Additionally, based on the finding of higher cpDNA diversity and older cpDNA lineages in NS, we propose that multiple founder events occurred in NS, while only a single lineage gave rise to current populations in the United States. CONCLUSIONS: By understanding how S. kennedyana responded to past shifts in climate and by identifying areas of high genetic diversity in the northern range edge, we discuss the potential response of the species to future climate change scenarios.

Host-plant dependent population genetics of the invading weevil Hypera postica.

Population genetics of invading pests can be informative for understanding their ecology. In this study, we investigated population genetics of the invasive alfalfa weevil Hypera postica in Fukuoka Prefecture, Japan. We analyzed mitochondrial tRNALeu-COII, nuclear EF-1α gene fragments, and Wolbachia infection in relation to three leguminous host plants: Vicia angustifolia, Vicia villosa, and a new host Astragalus sinicus cultivated as a honey source and green manure crop. A parsimony network generated from mitochondrial gene sequences uncovered two major haplotypic groups, Western and Egyptian. In contrast to reported Wolbachia infection of the Western strain in the United States, none of our analyzed individuals were infected. The absence of Wolbachia may contribute to the stable coexistence of mitochondrial strains through inter-strain reproductive compatibility. Hypera postica genetic variants for the mitochondrial and nuclear genes were associated neither with host plant species nor with two geographic regions (Hisayama and Kama) within Fukuoka. Mitochondrial haplogroups were incongruent with nuclear genetic variants. Genetic diversity at the nuclear locus was the highest for the populations feeding on V. angustifolia. The nuclear data for A. sinicus-feeding populations indicated past sudden population growth and extended Bayesian skyline plot analysis based on the mitochondrial and nuclear data showed that the growth of A. sinicus-feeding population took place within the past 1000 years. These results suggest a shorter history of A. sinicus as a host plant compared with V. angustifolia and a recent rapid growth of H. postica population using the new host A. sinicus.

Eco-evolutionary factors that influence its demographic oscillations in Prochilodus costatus (Actinopterygii: Characiformes) populations evidenced through a genetic spatial-temporal evaluation.

The human activity impact on wild animal populations is indicated by eco-evolutionary and demographic processes, along with their survival and capacity to evolve; consequently, such data can contribute toward enhancing genetic-based conservation programs. In this context, knowledge on the life-history and the eco-evolutionary processes is required to understand extant patterns of population structure in Prochilodus costatus a Neotropical migratory fish that has been threatened due to loss and fragmentation of its natural habitat since 1960s promoted by the expansion of hydroelectric power plant construction programs. This study evaluated the eco-evolutionary parameters that cause oscillations in the demography and structure of P. costatus populations. An integrated approach was used, including temporal and spatial sampling, next-generation sequencing of eight microsatellite loci, multivariate genetic analysis, and demographic life-history reconstruction. The results provided evidence of the complex interplay of ecological-evolutionary and human-interference events on the life history of this species in the upper basin. In particular, spawning wave behavior might have ecological triggers resulting in an overlapping of distinct genetic generations, and arising distinct migratory and nonmigratory genetic patterns living in the same area. An abrupt decrease in the effective population size of the P. costatus populations in the recent past (1960-80) was likely driven by environment fragmentation promoted by the construction of the Três Marias hydropower dam. The low allelic diversity that resulted from this event is still detected today; thus, active stocking programs are not effective at expanding the genetic diversity of this species in the river basin. Finally, this study highlights the importance of using mixed methods to understand spatial and temporal variation in genetic structure for effective mitigation and conservation programs for threatened species that are directly affected by human actions.

Genetic signatures of lineage fusion closely resemble population decline.

Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline-high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (F S and Z nS), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.

Mitochondrial DNA variation reveals maternal origins and demographic dynamics of Ethiopian indigenous goats.

The Horn of Africa forms one of the two main historical entry points of domestics into the continent and Ethiopia is particularly important in this regard. Through the analysis of mitochondrial DNA (mtDNA) d-loop region in 309 individuals from 13 populations, we reveal the maternal genetic variation and demographic dynamics of Ethiopian indigenous goats. A total of 174 variable sites that generated 231 haplotypes were observed. They defined two haplogroups that were present in all the 13 study populations. Reference haplotypes from the six globally defined goat mtDNA haplogroups show the two haplogroups present in Ethiopia to be A and G, the former being the most predominant. Although both haplogroups are characterized by an increase in effective population sizes (Ne) predating domestication, they also have experienced a decline in Ne at different time periods, suggesting different demographic histories. We observed seven haplotypes, six were directly linked to the central haplotypes of the two haplogroups and one was central to haplogroup G. The seven haplotypes were common between Ethiopia, Kenya, Egypt, and Saudi Arabia populations, suggesting common maternal history and the introduction of goats into East Africa via Egypt and the Arabian Peninsula, respectively. While providing new mtDNA data from a historically important region, our results suggest extensive intermixing of goats mediated by human socio-cultural and economic interactions. These have led to the coexistence of the two haplogroups in different geographic regions in Ethiopia resulting in a large caprine genetic diversity that can be exploited for genetic improvement.

The substitution rate of HIV-1 subtypes: a genomic approach.

HIV-1M causes most infections in the AIDS pandemic. Its genetic diversity is defined by nine pure subtypes and more than sixty recombinant forms. We have performed a comparative analysis of the evolutionary rate of five pure subtypes (A1, B, C, D, and G) and two circulating recombinant forms (CRF01_AE and CRF02 AG) using data obtained from nearly complete genome coding sequences. Times to the most recent common ancestor (tMRCA) and substitution rates of these HIV genomes, and their genomic partitions, were estimated by Bayesian coalescent analyses. Genomic substitution rate estimates were compared between the HIV-1 datasets analyzed by means of randomization tests. Significant differences in the rate of evolution were found between subtypes, with subtypes C and A1 and CRF01_AE displaying the highest rates. On the other hand, CRF02_AG and subtype D were the slowest evolving types. Using a different molecular clock model for each genomic partition led to more precise tMRCA estimates than when linking the same clock along the HIV genome. Overall, the earliest tMRCA corresponded to subtype A1 (median = 1941, 95% HPD = 1943-55), whereas the most recent tMRCA corresponded to subtype G and CRF01_AE subset 3 (median = 1971, 95% HPD = 1967-75 and median = 1972, 95% HPD = 1970-75, respectively). These results suggest that both biological and epidemiological differences among HIV-1M subtypes are reflected in their evolutionary dynamics. The estimates obtained for tMRCAs and substitution rates provide information that can be used as prior distributions in future Bayesian coalescent analyses of specific HIV-1 subtypes/CRFs and genes.

Tracing the epidemic history of hepatitis C virus genotypes in Saudi Arabia.

HCV genotype 4 is highly prevalent in many Middle Eastern countries, yet little is known about the genotype's epidemic history at the subtype-level in this region. To address the dearth of data from Saudi Arabia (SA) we genotyped 230 HCV isolates in the core/E- and NS5B-region and analyzed using Bayesian phylogenetic approaches. HCV genotype 4 (HCV/4) was positive in 61.7% (142/230) of isolates belonging to 7 different subtypes with the predominance of 4d (73/142; 51.4%) followed by 4a (51/142; 35.9%). Phylogenetic analysis also revealed a distinct epidemiological cluster of HCV/4d for Saudi Arabia. HCV/1 appeared as the second most prevalent genotype positive in 31.3% (72/230) of isolates with the predominance of 1b (53/72; 73.6%) followed by 1a (16/72; 22.2%), and 1g (3/72; 4.1%). A small proportion of isolates belonged to HCV/3a (12/230; 5.2%), and HCV/2a (4/230; 1.7%). We estimate that the genotype 4 common ancestor existed around 1935 (1850-1985). Genotype 4 originated plausibly in Central Africa and multiple subtypes disseminated across African borders since ~1970, including subtype 4d which dominates current HCV infections in Saudi Arabia. The Bayesian skyline plot (BSP) analysis showed that genotype 4d entered the Saudi population in 1900. The effective number of HCV infections grew gradually until the second half of the 1950s and more rapidly until the early-80s through the use of imported blood units and blood products. Subsequently, the rate of HCV infection in the Saudi Arabian population was stabilized through effective screening of blood and infection control measures.

Postglacial range shift and demographic expansion of the marine intertidal snail Batillaria attramentaria.

To address the impacts of past climate changes, particularly since the last glacial period, on the history of the distribution and demography of marine species, we investigated the evolutionary and demographic responses of the intertidal batillariid gastropod, Batillaria attramentaria, to these changes, using the snail as a model species in the northwest Pacific. We applied phylogeographic and divergence population genetic approaches to mitochondrial COI sequences from B. attramentaria. To cover much of its distributional range, 197 individuals collected throughout Korea and 507 publically available sequences (mostly from Japan) were used. Finally, a Bayesian skyline plot (BSP) method was applied to reconstruct the demographic history of this species. We found four differentiated geographic groups around Korea, confirming the presence of two distinct, geographically subdivided haplogroups on the Japanese coastlines along the bifurcated routes of the warm Tsushima and Kuroshio Currents. These two haplogroups were estimated to have begun to split approximately 400,000 years ago. Population divergence analysis supported the hypothesis that the Yellow Sea was populated by a northward range expansion of a small fraction of founders that split from a southern ancestral population since the last glacial maximum (LGM: 26,000-19,000 years ago), when the southern area became re-submerged. BSP analyses on six geographically and genetically defined groups in Korea and Japan consistently demonstrated that each group has exponentially increased approximately since the LGM. This study resolved the phylogeography of B. attramentaria as a series of events connected over space and time; while paleoceanographic conditions determining the connectivity of neighboring seas in East Asia are responsible for the vicariance of this species, the postglacial sea-level rise and warming temperatures have played a crucial role in rapid range shifts and broad demographic expansions of its populations.

Accounting for rate variation among lineages in comparative demographic analyses.

Genetic analyses of contemporary populations can be used to estimate the demographic histories of species within an ecological community. Comparison of these demographic histories can shed light on community responses to past climatic events. However, species experience different rates of molecular evolution, and this presents a major obstacle to comparative demographic analyses. We address this problem by using a Bayesian relaxed-clock method to estimate the relative evolutionary rates of 22 small mammal taxa distributed across northwestern North America. We found that estimates of the relative molecular substitution rate for each taxon were consistent across the range of sampling schemes that we compared. Using three different reference rates, we rescaled the relative rates so that they could be used to estimate absolute evolutionary timescales. Accounting for rate variation among taxa led to temporal shifts in our skyline-plot estimates of demographic history, highlighting both uniform and idiosyncratic evolutionary responses to directional climate trends for distinct ecological subsets of the small mammal community. Our approach can be used in evolutionary analyses of populations from multiple species, including comparative demographic studies.

Genetic signatures of a demographic collapse in a large-bodied forest dwelling primate (Mandrillus leucophaeus).

It is difficult to predict how current climate change will affect wildlife species adapted to a tropical rainforest environment. Understanding how population dynamics fluctuated in such species throughout periods of past climatic change can provide insight into this issue. The drill (Mandrillus leucophaeus) is a large-bodied rainforest adapted mammal found in West Central Africa. In the middle of this endangered monkey's geographic range is Lake Barombi Mbo, which has a well-documented palynological record of environmental change that dates to the Late Pleistocene. We used a Bayesian coalescent-based framework to analyze 2,076 base pairs of mitochondrial DNA across wild drill populations to infer past changes in female effective population size since the Late Pleistocene. Our results suggest that the drill underwent a nearly 15-fold demographic collapse in female effective population size that was most prominent during the Mid Holocene (approximately 3-5 Ka). This time period coincides with a period of increased dryness and seasonality across Africa and a dramatic reduction in forest coverage at Lake Barombi Mbo. We believe that these changes in climate and forest coverage were the driving forces behind the drill population decline. Furthermore, the warm temperatures and increased aridity of the Mid Holocene are potentially analogous to current and future conditions faced by many tropical rainforest communities. In order to prevent future declines in population size in rainforest-adapted species such as the drill, large tracts of forest should be protected to both preserve habitat and prevent forest loss through aridification.