Population expansion

Given the difficulty of separating the three Picea species—P. glauca, P. mariana, and P. rubens (white, black, and red spruce)—in the pollen record, little is known about their unique histories in eastern North America following deglaciation. Here we report the first use of a classification tree analysis (CART) to distinguish pollen grains of these species. It was successfully applied to fossil pollen from eight sites in Maine and one in Massachusetts. We focused on the late glacial/early Holocene (14,000 to 8000 cal yr B.P.) and the late Holocene (1400 cal yr B.P. to present)—the two key periods since deglaciation when Picea has been abundant in the region. The result shows a shift from a Picea forest of P. glauca and P. mariana in the late glacial to a forest of P. rubens and P. mariana in the late Holocene. The small number of P. rubens grains identified from the late glacial/early Holocene samples…

With a total population of less than 60 individuals limited to two locations, the Javan rhinoceros is perhaps the most endangered large mammal on earth. Although species specific information is crucial to its conservation, its precarious status, habitat inaccessibility, and behavioral adaptations pose major obstacles to its study. Here we report on the first genetic analysis of the two extant populations, in Ujung Kulon, Indonesia, and Cat Tien, Vietnam, and discuss their conservation. As its critically endangered status precluded invasive sampling, we extracted DNA from dung, amplifying and sequencing segments of the mtDNA 12S rRNA gene and the non-coding D-loop. Divergence between Javan rhinos from Ujung Kulon and Cat Tien was similar to that between recognized subspecies of African rhinos, and exceeded that between Sumatran rhinos. The Ujung Kulon and Cat Tien populations represent separate Evolutionary Significant Units, advocating independent management. However, given the precariousness of the Cat Tien population, demographic considerations may override genetic issues in the short term. Genetic diversity of Javan rhinos was low and population expansion in the immediate future will be critical for its survival.

A detailed analysis of the location and composition of Iberian vegetation types during the whole Pleistocene and Holocene periods shows a complex patched landscape with persistence of different types of ecosystems, even during glacial times. In addition, recent, high-resolution palaeoecological records are changing the traditional picture of post-glacial vegetation succession in the Iberian Peninsula. The main available charcoal and pollen sequences include, coniferous and deciduous forest, steppes, shrublands, savannahs and glacial refugia during the Pleistocene for Meso-thermophytes (phytodiversity reservoirs), in different proportions. This panorama suggests an environmental complexity that relates biotic responses to climate changes forced by Milankovitch cycles, suborbital forcings and by the latitudinal and physiographic particularities of the Iberian Peninsula. Thus, many factors are critical in the course of vegetational developments and strong regional differences are obser...

Intensification of agriculture and irrigation are often considered triggers for both the flourishing and demise of civilizations. Was irrigation a key factor of state formation and urban development in northern Ethiopia? We argue that a household-based management of farmland and water would have provided a strategy sustainable over the long term and flexible enough to adjust to population expansion and contraction at the ancient capital of the Kingdom of Aksum (first millennium ad). This conclusion is based on research into environmental, archaeological and historical data concerning the forms and use of water resources together with new information originating from geoarchaeological and palaeobotanical work in the Aksum area. The results indicate that the characteristics of the environment and traditional farming system are such that intensive irrigation works were not necessary. It appears likely that ancient Aksumites utilized seasonal rainfall and water conservation methods to sustain food production.

The excess of rare variants in global sequencing studies of the nonrecombining portion of the Y chromosome (NRY) has been interpreted as evidence for the effects of human demographic expansion. However, many NRY polymorphisms are geographically localized and the effect of different geographical sampling on patterns of NRY variation is unknown. We use two sampling designs to detect population structure and its effects on patterns of human NRY polymorphism. First, we sequence 26.5 kb of noncoding Y chromosome DNA from 92 globally distributed males representing 35 populations. We find that the number of polymorphisms with singleton variants is positively correlated with the number of populations sampled and that there is a significant negative correlation of Tajima's D (TD) and Fu and Li's D (FD) statistics with the number of pooled populations. We then sequence the same region in a total of 73 males sampled from 3 distinct populations and find that TD and FD values for the 3 p...

Within the next decade, China’s labour force will begin to contract, while that of India will expand faster than its population. Relative labour abundance will bring higher capital returns and an increasing share of global FDI to India. Yet China may relax its One Child Policy further and India’s fertility could follow the pattern elsewhere in Asia and decline faster

Mesoamerica, defined as the broad linguistic and cultural area from middle southern Mexico to Costa Rica, might have played a pivotal role during the colonization of the American continent. The Mesoamerican isthmus has constituted an important geographic barrier that has severely restricted gene flow between North and South America in pre-historical times. Although the Native American component has been already described in admixed Mexican populations, few studies have been carried out in native Mexican populations. In this study, we present mitochondrial DNA (mtDNA) sequence data for the first hypervariable region (HVR-I) in 477 unrelated individuals belonging to 11 different native populations from Mexico. Almost all of the Native Mexican mtDNAs could be classified into the four pan-Amerindian haplogroups (A2, B2, C1, and D1); only two of them could be allocated to the rare Native American lineage D4h3. Their haplogroup phylogenies are clearly star-like, as expected from relatively young populations that have experienced diverse episodes of genetic drift (e.g., extensive isolation, genetic drift, and founder effects) and posterior population expansions. In agreement with this observation, Native Mexican populations show a high degree of heterogeneity in their patterns of haplogroup frequencies. Haplogroup X2a was absent in our samples, supporting previous observations where this clade was only detected in the American northernmost areas. The search for identical sequences in the American continent shows that, although Native Mexican populations seem to show a closer relationship to North American populations, they cannot be related to a single geographical region within the continent. Finally, we did not find significant population structure in the maternal lineages when considering the four main and distinct linguistic groups represented in our Mexican samples (Oto-Manguean, Uto-Aztecan, Tarascan, and Mayan), suggesting that genetic divergence predates linguistic diversification in Mexico.

Evolutionary relationships of the tree frogs from the Middle East and the demographic histories of their populations were studied using a combination of mitochondrial and nuclear genes. Hyla savignyi and neighboring populations of H. orientalis (former eastern populations of H. arborea) were the main focus taxa. Within H. savignyi, a deep phylogenetic divergence dated about 8.4Ma was discovered. Southern populations from Yemen, Jordan, southern Syria and extreme north-eastern Israel are hereby described as a new species, H. felixarabica sp. nov. Our study points to a biogeographic connection of the south-western Arabian Peninsula and southern Levant and to the importance of the Dead Sea Rift as a historical barrier geographically separating the new species from H. savignyi. Major genetic breaks revealed within species (H. felixarabica: Yemen vs. Jordan-Syria; H. savignyi sensu stricto: Levant vs. Turkey-Iran) are probably connected to climate changes during the Plio-Pleistocene boun...

Human mediated biological invasions are seen as an increasing danger for biodiversity. On the other hand, range expansions are natural processes. It is often practically not possible to tell these processes apart, like in the case of the freshwater crab Potamon fluviatile. This species has a disjunct distribution on the Balkan Peninsula, Italy, Sicily and Malta. An innovative analysis framework involving phylogeographic model selection and temporal coalescent analyses on a mitochondrial dataset (COI and NADH1) could clarify that the origin of the species was on the Balkans and the colonisation of Italy proceeded from the northern Balkans via southern Italy in the Otranto Strait region. The population expansion associated with this invasion was estimated to have taken place 15,000 years before present (95% c.f. 10,000–24,000 years BP). An anthropogenic introduction is therefore implausible and a natural expansion likely. We argue that the species should thus be included in the national conservation management in Italy.

The population genetic diversity and demographic history of the longtail tuna Thunnus tonggol in Malaysian waters was investigated using mitochondrial DNA D-loop and NADH dehydrogenase subunit 5 (ND5). A total of 203 (D-loop) and 208 (ND5) individuals of T. tonggol were sampled from 11 localities around the Malaysian coastal waters. Low genetic differentiation between populations was found, possibly due to the past demographic history, dispersal potential during egg and larval stages, seasonal migration in adults, and lack of geographical barriers. The gene trees, constructed based on the maximum likelihood method, revealed a single panmictic population with unsupported internal clades, indicating an absence of structure among the populations studied. Analysis on population pairwise comparison Ф ST suggested the absence of limited gene flow among study sites. Taken all together, high haplotype diversity (D-loop = 0.989-1.000; ND5 = 0.848-0.965), coupled with a low level of nucleotide diversity (D-loop = 0.019-0.025; ND5 = 0.0017-0.003), "star-like" haplotype network, and unimodal mismatch distribution, suggests a recent population expansion for populations of T. tonggol in Malaysia. Furthermore, neutrality and goodness of fit tests supported the signature of a relatively recent population expansion during the Pleistocene epoch. To provide additional insight into the phylogeographic pattern of the species within the Indo-Pacific Ocean, we included haplotypes from GenBank and a few samples from Taiwan. Preliminary analyses suggest a more complex genetic demarcation of the species than an explicit Indian Ocean versus Pacific Ocean delineation.

Aim To determine the relationships between otter (Lutra lutra) distribution dynamics and environmental and spatial constraints over a 20-year period.
Location Andalusia, southern Iberian Peninsula.
Methods We synthesized otter distribution data from three otter surveys (1985, 1995 and 2005) using subcatchment areas defined by hydrological barriers. Subcatchments were characterized by two ‘natural’ (climatic and orographic variables) and two ‘human’ (land use and population density) gradients. In addition, we calculated two contagion variables (the distance to previously occupied subcatchments and the percentage of occupied subcatchments within a 50 km buffer) for consecutively surveyed subcatchments.
Results Between 1985 and 2005 the percentage of subcatchments with otters present increased from 42% to 72%. Otters tended to be rare or absent from human-dominated areas. Anthropogenic gradients were better predictors of otter distribution than natural ones. Human and natural gradients showed strong covariation, but for any value of the natural gradients otters tended to be present in subcatchments with lower human impacts. Colonization of new subcatchments was found to be strongly related to contagion variables and expansion rates were slower than those estimated in other studies. Newly colonized areas tended to be located in areas with intermediate human influence, while repeated absences occurred mainly in areas where human impact was most severe.
Main conclusions Our results suggest that recent otter expansion across Andalusia is a reflection of large-scale improvement in environmental conditions. Otter populations that survived the period of strong and generalized declines appear to be acting as sources from which neighbouring areas are colonized, probably aided by improved water quality and increases in food availability. However, the further expansion of otters into their full original range is likely to be constrained by human-impacted landscapes.

A detailed analysis of the location and composition of Iberian vegetation types during the whole Pleistocene and Holocene periods shows a complex patched landscape with persistence of different types of ecosystems, even during glacial times. In addition, recent, high-resolution palaeoecological records are changing the traditional picture of post-glacial vegetation succession in the Iberian Peninsula. The main available charcoal and pollen sequences include, coniferous and deciduous forest, steppes, shrublands, savannahs and glacial refugia during the Pleistocene for Meso-thermophytes (phytodiversity reservoirs), in different proportions. This panorama suggests an environmental complexity that relates biotic responses to climate changes forced by Milankovitch cycles, suborbital forcings and by the latitudinal and physiographic particularities of the Iberian Peninsula. Thus, many factors are critical in the course of vegetational developments and strong regional differences are obser...

The Sierra Nevada of southern Spain is a landscape with a rich biological and cultural heritage. The range was extensively glaciated during the late Pleistocene. However, the postglacial paleoecologic history of the highest range in southern Europe is nearly completely unknown. Here we use sediments from a small lake above present treeline – Laguna de Río Seco at 3020 m elevation – in a paleoecological study documenting over 11,500 calendar years of vegetation, fire and climate change, addressing ecological and paleoclimatic issues unique to this area through comparison with regional paleoecological sequences. The early record is dominated by Pinus pollen, with Betula, deciduous Quercus, and grasses, with an understory of shrubs. It is unlikely that pine trees grew around the lake, and fire was relatively unimportant at this site during this period. Aquatic microfossils indicate that the wettest conditions and highest lake levels at Laguna de Río Seco occurred before 7800 cal yr BP. This is in contrast to lower elevation sites, where wettest conditions occurred after ca 7800. Greater differences in early Holocene seasonal insolation may have translated to greater snowpack and subsequently higher lake levels at higher elevations, but not necessarily at lower elevations, where higher evaporation rates prevailed. With declining seasonality after ca 8000 cal yr BP, but continuing summer precipitation, lake levels at the highest elevation site remained high, but lake levels at lower elevation sites increased as evaporation rates declined. Drier conditions commenced regionally after ca 5700 cal yr BP, shown at Laguna de Río Seco by declines in wetland pollen, and increases in high elevation steppe shrubs common today (Juniperus, Artemisia, and others). The disappearance or decline of mesophytes, such as Betula from ca 4000 cal yr BP is part of a regional depletion in Mediterranean Spain and elsewhere in Europe from the mid to late Holocene. On the other hand, Castanea sativa increased in Laguna de Río Seco record after ca 4000 cal yr BP, and especially in post-Roman times, probably due to arboriculture. Though not as important at high than at low elevations, fire occurrence was elevated, particularly after ca 3700 years ago, in response to regional human population expansion. The local and regional impact of humans increased substantially after ca 2700 years ago, with the loss of Pinus forest within the mountain range, increases in evidence of pasturing herbivores around the lake, and Olea cultivation at lower elevations. Though human impact was not as extensive at high elevation as at lower elevation sites in southern Iberia, this record confirms that even remote sites were not free of direct human influence during the Holocene.► We investigate high elevation vegetation change through time in southern Spain. ► Laguna de Río Seco documents regional environmental change for southern Spain. ► The early Holocene monsoonal climate ended earlier here than at lower elevations. ► Late Holocene human impact may have been limited to grazing around the lake. ► Record shows even remote sites were not free of human influence during the Holocene.