Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range‐wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil‐calibrated and rate‐calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide‐ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well‐supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co‐distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid‐adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 949–967.     

山东青岛大珠山遗址晚更新世人类活动的环境背景

大珠山遗址是青岛市首个具有地层依据的旧石器遗址。该遗址的发掘不仅丰富了我国沿海地区的旧石器考古材料,更对探讨早期人类的生存适应和迁移扩散等问题具有深远意义。解译遗址中的环境背景信息,可以帮助我们更准确地理解当时人类的生存状态。本文通过花粉和磁化率等指标,重建了该遗址所在区域的环境演变过程。研究结果显示:1)大珠山遗址的光释光年龄为65.7-52.9ka,对应MIS4-MIS3c;2)从MIS5b到MIS3b(86.0-45.0ka),区域植被经历4个演替阶段,依次为落叶林草原、落叶阔叶林草原、温带草原和疏林草原,其反映的气候趋势与区域背景下的环境变化过程基本一致;3)MIS4-MIS3c期间迅速回暖的气候,稳定适宜的生存环境,均为早期人类的活动提供良好的生态背景。随后气候转冷,海岸线后退,该地区的人类遗存明显减少,可能指示人类活动减弱或者迁出。这种不同时期内的人类活动强度的变化,表明气候主控下的生存环境变化深刻影响着近海地区早期人类的适应策略。     

Diversification patterns in the CES clade (Brassicaceae tribes Cremolobeae,Eudemeae, Schizopetaleae) in Andean South America

Dated molecular phylogenetic trees show that the Andean uplift had a major impact on South American biodiversity. For many Andean groups, accelerated diversification (radiation) has been documented. However, not all Andean lineages appear to have diversified following the model of rapid radiation, particularly in the central and southern Andes. Here, we investigated the diversification patterns for the largest South American‐endemic lineage of Brassicaceae, composed of tribes Cremolobeae, Eudemeae and Schizopetaleae (CES clade). Species of this group inhabit nearly all Andean biomes and adjacent areas including the Atacama–Sechura desert, the Chilean Matorral and the Patagonian Steppe. First, we studied diversification times and historical biogeography of the CES clade. Second, we analysed diversification rates through time, lineages and associated life forms. Results demonstrate that early diversification of the CES clade occurred in the early to mid‐Miocene (c. 12–19 Mya) and involved the central Andes, the southern Andes and the Patagonian Steppe, and the Atacama–Sechura desert. The Chilean Matorral and northern Andes were colonized subsequently in the early Pliocene (4–5 Mya). Diversification of the CES clade was recovered as a gradual process without any evidence for rate shifts or rapid radiation, in contrast to many other Andean groups analysed so far. Diversification time/rates and biogeographical patterns obtained for the CES clade are discussed and compared with patterns and conclusions reported for other Andean plant lineages.     

Scalariform-to-simple transition in vessel perforation plates triggered by differences in climate during the evolution of Adoxaceae

Background and Aims Angiosperms with simple vessel perforations have evolved many times independently of species having scalariform perforations, but detailed studies to understand why these transitions in wood evolution have happened are lacking. We focus on the striking difference in wood anatomy between two closely related genera of Adoxaceae, Viburnum and Sambucus, and link the anatomical divergence with climatic and physiological insights.Methods After performing wood anatomical observations, we used a molecular phylogenetic framework to estimate divergence times for 127 Adoxaceae species. The conditions under which the genera diversified were estimated using ancestral area reconstruction and optimization of ancestral climates, and xylem-specific conductivity measurements were performed.Key Results Viburnum, characterized by scalariform vessel perforations (ancestral), diversified earlier than Sambucus, having simple perforations (derived). Ancestral climate reconstruction analyses point to cold temperate preference for Viburnum and warm temperate for Sambucus. This is reflected in the xylem-specific conductivity rates of the co-occurring species investigated, showing that Viburnum lantana has rates much lower than Sambucus nigra.Conclusions The lack of selective pressure for high conductive efficiency during early diversification of Viburnum and the potentially adaptive value of scalariform perforations in frost-prone cold temperate climates have led to retention of the ancestral vessel perforation type, while higher temperatures during early diversification of Sambucus have triggered the evolution of simple vessel perforations, allowing more efficient long-distance water transport.     

Closing the gap between rocks and clocks using total-evidence dating

Total-evidence dating (TED) allows evolutionary biologists to incorporate a wide range of dating information into a unified statistical analysis. One might expect this to improve the agreement between rocks and clocks but this is not necessarily the case. We explore the reasons for such discordance using a mammalian dataset with rich molecular, morphological and fossil information. There is strong conflict in this dataset between morphology and molecules under standard stochastic models. This causes TED to push divergence events back in time when using inadequate models or vague priors, a phenomenon we term ‘deep root attraction’ (DRA). We identify several causes of DRA. Failure to account for diversified sampling results in dramatic DRA, but this can be addressed using existing techniques. Inadequate morphological models also appear to be a major contributor to DRA. The major reason seems to be that current models do not account for dependencies among morphological characters, causing distorted topology and branch length estimates. This is particularly problematic for huge morphological datasets, which may contain large numbers of correlated characters. Finally, diversification and fossil sampling priors that do not incorporate all the available background information can contribute to DRA, but these priors can also be used to compensate for DRA. Specifically, we show that DRA in the mammalian dataset can be addressed by introducing a modest extra penalty for ghost lineages that are unobserved in the fossil record, for instance by assuming rapid diversification, rare extinction or high fossil sampling rate; any of these assumptions produces highly congruent divergence time estimates with a minimal gap between rocks and clocks. Under these conditions, fossils have a stabilizing influence on divergence time estimates and significantly increase the precision of those estimates, which are generally close to the dates suggested by palaeontologists.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.     

An underground burst of diversity – a new look at the phylogeny and taxonomy of the genus Talpa Linnaeus, 1758 (Mammalia: Talpidae) as revealed by nuclear and mitochondrial genes

Using both nuclear and mitochondrial sequences, we demonstrate high genetic differentiation in the genus Talpa and confirm the existence of cryptic species in the Caucasus and Anatolia, namely, T. talyschensis Vereschagin, 1945, T. ognevi Stroganov, 1948, and Talpa ex gr. levantis. Our data support four clades in the genus Talpa that showed strong geographical associations. The ‘europaea’ group includes six species from the western portion of the genus' range (T. europaea, T. occidentalis, T. romana, T. caeca, T. stankovici, and T. levantis s.l.); another three groups are distributed further east: the ‘caucasica’ group (Caucasus), the ‘davidiana’ group (eastern Anatolia and Elburz) and T. altaica (Siberia). The phylogenetic position of T. davidiana was highlighted for the first time. The order of basal branching remains controversial, which can be attributed to rapid diversification events. The molecular time estimates based on nuclear concatenation estimated the basal divergence of the crown Talpa during the latest Miocene. A putative scenario of Talpa radiation and issues of species delimitation are discussed. © 2015 The Linnean Society of London     

Luminescence in Li2BaP2O7

The photo‐, thermo‐ and optically stimulated luminescence in Li₂BaP₂O₇ activated with Eu²⁺/Cu⁺ are reported. Strong thermoluminescence, which is about two times greater than LiF‐TLD 100 was observed in the Eu²⁺‐activated sample. It also exhibited optically stimulated luminescence sensitivity of ~20% that of commercial Al₂O₃:C phosphor. Copyright © 2014 John Wiley & Sons, Ltd.