Holarctic genetic structure and range dynamics in the woolly mammoth

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred.     

Late Pleistocene divergence and postglacial expansion in the Brazilian Atlantic Forest: multilocus phylogeography of Rhopias gularis (Aves: Passeriformes)

In the last decade, phylogeographic studies have revealed a complex evolutionary history of the Brazilian Atlantic Forest (AF) biota. Here, we investigated the evolutionary history of Rhopias gularis, an endemic bird of the AF, based on sequences of two mitochondrial genes and three nuclear introns from 64 specimens from 15 localities. We addressed three main questions: (1) Does the genetic diversity of R. gularis exhibit a distribution pattern congruent with the refuge hypothesis postulated for the AF? (2) Is the population genetic structure of R. gularis congruent with those observed in other AF species? (3) What were the possible historical events responsible for the population structure of this species? Our mtDNA data revealed two phylogroups: (1) phylogroup central‐south, with samples from the central and southern parts of the range; (2) and phylogroup north, which included individuals from southern Bahia. Nevertheless, nuclear loci did not reveal any evidence of population structure. Bottleneck tests indicated that the central‐south lineage experienced demographic expansion, starting around 20 kya, which coincides with the end of the last glacial maximum. However, there was no evidence of population growth in phylogroup north. Isolation with migration analysis indicated that these phylogroups split c.a. 304 kya, with limited gene flow among them. Palaeodistribution models indicated that R. gularis had a reduced distribution in the south and central AF during the last glacial maximum. Our results support a diversification scenario that is in accordance with proposed Pleistocene refugia. The phylogeographic results from our study exhibited spatial and temporal concordances and discordances with previous studies of organisms from the AF. Differences in habitat requirements of these species could be behind this complex scenario. Future studies correlating variables of the niche of these species with the observed phylogeographic patterns may help understand why there are congruent and incongruent results.     

Pleistocene survival on central Alpine nunataks: genetic evidence from the jumping bristletail Machilis pallida

Mechanisms of survival during the Pleistocene glaciation periods have been studied for more than a century. Until now, molecular studies that confirmed animal survival on Alpine nunataks, that is, ice‐free summits surrounded by glaciers, were restricted to peripheral areas. Here, we search for molecular signatures of inner‐Alpine survival of the narrow endemic and putatively parthenogenetic Alpine jumping bristletail Machilis pallida combining mitochondrial and AFLP data from its three known populations. The mitochondrial data indicate survival on both peripheral and central nunataks, the latter suggesting that refugia in the centre of the Alpine main ridge were more widespread than previously recognized. Incongruences between mitochondrial and AFLP patterns suggest a complex evolutionary history of the species and may be explained via parallel fixation of parthenogenesis of different origins during the last glacial maximum. We suggest that the inferred parthenogenesis may have been essential for central nunatak survival, but may pose a serious threat for M. pallida in consideration of the present climatic changes.     

中国梭梭属植物历史分布格局及其驱动机制

梭梭属(Haloxylon)植物是藜科的古老孑遗物种, 探究末次间冰期(last interglacial period, LIG)和末次盛冰期(last glacial maximum period, LGM)以来中国梭梭属植物的历史地理分布格局及其驱动机制, 对了解气候变化背景下旱生植物区系的发展与演化具有重要意义。本研究利用梭梭属85个自然分布点数据(60条梭梭(Haloxylon ammodendron)分布记录、25条白梭梭(H. persicum)分布记录)和2套环境因子数据, 整合GIS空间分析和9种物种分布模型, 分析了梭梭属末次间冰期以来的地理分布格局变化及其驱动机制。基于62个梭梭属种群的叶绿体基因测序数据, 利用最小成本路径方法, 模拟了末次间冰期以来梭梭属可能的扩散路径。利用R软件prcomp函数对影响梭梭属分布的环境变量进行主成分分析(principal component analysis, PCA), 评价了环境变量对梭梭属适宜分布的贡献, 并分析了关键变量与分布适宜性的相关性。结果表明: (1)集成模型的模拟精度较单一模型显著提升, 且对白梭梭的模拟精度高于梭梭; (2)末次间冰期以来, 梭梭属植物的分布均经历了显著收缩和冰后期扩张, 末次间冰期至末次盛冰期时期, 在准噶尔盆地、塔里木盆地西部广泛分布的梭梭大面积向西退缩至避难所(准噶尔盆地西北缘和塔里木盆地西北缘); 白梭梭从准噶尔盆地、塔里木盆地西端向南退缩至避难所(准噶尔盆地南缘); 末次盛冰期至今, 梭梭向东沿甘肃北部扩张直至内蒙古西部阿拉善荒漠, 白梭梭向东北方向小范围扩张, 占据了准噶尔盆地西部和南缘; (3)末次间冰期以来的气候波动对梭梭属植物的分布存在较大限制, 降水因子主导了梭梭属适宜分布面积的变化, 温度因子影响了梭梭属分布适宜性的高低。     

Phylogeographic analyses suggest that a deciduous species (Ostryopsis davidiana Decne., Betulaceae) survived in northern China during the Last Glacial Maximum

Aim Palaeontologial data suggest that all temperate forest species in northern China migrated southwards during the Last Glacial Maximum (LGM) and recolonized post‐glacially within the Holocene. We tested this assumption using phylogeographical studies of a temperate deciduous shrub species (Ostryopsis davidiana Decne., Betulaceae), which has a wide distribution in northern China. Location Northern China. Methods We sequenced two chloroplast DNA (cpDNA) fragments (trnL–trnF and psbA–trnH, together about 1300 bp in length) of 294 plants from 21 populations across the total distribution range of this species. We used maximum parsimony and haplotype network methods to construct phylogenetic relationships among haplotypes. Results The analysis of cpDNA variation identified eight haplotypes. A single haplotype was fixed in all populations except for one population that was polymorphic, having two haplotypes. The population subdivisions were extremely high (G_ST = 0.972 and N_ST = 0.974), suggesting very low gene flow between populations. Haplotypes clustered into two tentative clades, both of which occur in the southern region of the species’ range but only one of which occurs in the northern region. Across the sampled populations, the haplotype distributions were differentiated geographically. Main conclusions Our analyses suggest that multiple refugia were maintained across the range of O. davidiana in both northern (north of the Qing Mountains) and southern (south of the Qing Mountains) regions during the LGM rather than that the species survived only in the south and subsequently colonized northwards. The extremely low within‐population diversity of this species suggests strong bottleneck or founder effects within each fragmented region during the Quaternary climatic oscillations. These findings provide important clues for understanding range shifts and changes in within‐ and/or between‐population genetic diversity of temperate forests in response to past climatic oscillations in northern China.     

Resilient forest faunal communities in South Africa: a legacy of palaeoclimatic change and extinction filtering?

Aim To examine the influence of climatic extinction filtering during the last glacial maximum (LGM; c. 18,000 yr bp ) and of the subsequent recolonization of forest faunas on contemporary assemblage composition in southern African forests. Location South Africa, Mozambique, Swaziland, Zimbabwe. Methods Data comprised presence/absence by quarter‐degree grid cell for forest‐dependent and forest‐associated birds, non‐volant mammals and frogs. Twenty‐one forest subregions were assigned to one of three previously identified forest types: Afrotemperate, scarp, and Indian Ocean coastal belt. Differences among forest types were examined through patterns and gradients of species richness and endemism, assemblage similarity, species turnover, and coefficients of species dispersal direction. The influence of contemporary environment on assemblage composition was investigated using partial canonical correspondence analysis. Several alternative biogeographical hypotheses for the recolonization of forest faunas were tested. Results Afrotemperate faunas are relatively species‐poor, have low species turnover, and are unsaturated and infiltrated by generalist species. In northern and central regions, communities are supplemented by recolonization from scarp forest refugia, and among frogs by autochthanous speciation in localized refugia. Scarp faunas are relatively species‐rich, contain many forest‐dependent species, have high species turnover, and overlap with coastal and Afrotemperate faunas. Coastal forests are relatively species‐rich with high species turnover. Main conclusions Afrotemperate communities were affected most by climatic extinction filtering events. Scarp forests were Afrotemperate refugia during the LGM and are a contemporary overlap zone between Afrotemperate and coastal forest. Coastal faunas derive from post‐LGM colonization along the eastern seaboard from tropical East African refugia. The greatest diversity is achieved in scarp and coastal forest faunas in northern KwaZulu–Natal province. This historical centre of diversity has influenced the faunal diversity of nearly all other forests in South Africa. The response of vertebrate taxa to large‐scale, historical processes is dependent on their relative mobility: forest birds best illustrate patterns resulting from post‐glacial faunal dispersal, while among mammals and frogs the legacy of climatic extinction filtering remains stronger.     

中国的骨针及其对晚更新世人类扩散的指示意义

在最近的一篇文章中,由d’Errico教授率领的来自中国、法国、德国研究者的工作表明,世界上最早的骨针出现于西伯利亚和中国北方地区,且这两个地区的骨针可能是独立起源。中国考古学的纪录为这一观点提供了更多的新证据。本文将这一工具类型与石器技术和环境背景结合考察,探讨更新世晚期后半段发生的人群的扩散。我们通过材料的梳理证明,中国北方地区的骨针,是出现于距今31000年前的一次技术创新,这一技术创新以石核-石片技术为代表的中国旧石器晚期的到来为背景。距今25000年,一种新形制的骨针出现。这些骨针形制扁平,与细石叶技术同时出现。这可能反映了欧亚大陆西方人群的东迁,这些人群带来了细石叶技术。更新世末,骨针更加多样化,这意味着他们可能有多种用途。在晚冰期末段,中国北方地区的骨针不仅与细石叶技术共出,同时也与石核、石片和陶器共出。在中国南方地区,在距今12000年前,骨针的出现与石核-石片技术同时出现。南方地区的骨针或是本地的的发明,或由末次冰期前北方人群的南迁带来的。长江以南地区,骨针与石核、石片和陶器在更新世晚期同时出现。更新世晚期中国南北方地区同时出现的这一工具组合,即石核、石片、陶器和骨针,预示着南北方地区在更新世晚期和全新世早期可能存在着长距离的人群的移动和文化的交流。     

Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100

Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.