Rome initiated several campaigns to expand, conquer, and enslave local Italic populations following the establishment of the republic in 504 BCE. However, the cultural and biological changes resulting from Roman subjugation across Italy remain a topic of intense historical debate. Although important, historic and archaeological lines of evidence fail to track the impact of forced enslavement and enculturation at individual and broader genetic scales and, more generally, offer fewer clues regarding the potential affinities of Roman period Italians to European, Near Eastern, western Asian and North African populations at this time.

Premise of the Study Pinaceae have a rich but enigmatic early fossil record, much of which is represented by permineralized seed cones. Our incomplete knowledge of morphology and anatomy in living and extinct species poses an important barrier to understanding their phylogenetic relationships and timing of diversification. Methods We expanded a morphology matrix to 46 fossil and 31 extant Pinaceae species, mainly adding characters from stem and leaf anatomy and seed cones. Using parsimony and Bayesian inference, we compared phylogenetic relationships for extant taxa with and without fossils from the morphology matrix combined with an alignment of plastid gene sequences. Key Results Combined analysis of morphological and molecular characters resulted in a phylogeny of extant Pinaceae that was robust at all nodes except those relating to the interrelationships of Pinus, Picea, and Cathaya and the position of Cedrus. Simultaneous analysis of all fossil and extant species did not result in changes in the relationships among the extant species but did greatly reduce branch support. We found that the placement of most fossils was sensitive to the method of phylogenetic reconstruction when analyzing them singly with the extant species. Conclusions A robust phylogenetic hypothesis for the main lineages of Pinaceae is emerging. Most Early Cretaceous fossils are stem or crown lineages of Pinus, but close relationships also were found between fossils and several other extant genera. The phylogenetic position of fossils broadly supports the existence of extant genera in the Lower Cretaceous.

Noninvasive sampling is an important development in population genetic monitoring of wild animals. Particularly, the collection of environmental DNA (eDNA) which can be collected without needing to encounter the target animal facilitates the genetic analysis of endangered species. One method that has been applied to these sample types is target capture and enrichment which overcomes the issue of high proportions of exogenous (nonhost) DNA from these lower quality samples. We tested whether target capture of mitochondrial DNA from sampled feeding traces of the aye-­aye, an endangered lemur species would yield mitochondrial DNA sequences for population genetic monitoring. We sampled gnawed wood where aye-­ayes excavate wood-b­ oring insect larvae from trees. We designed RNA probes complementary to the aye-­aye’s mitochondrial genome and used these to isolate aye-­aye DNA from other nontarget DNA in these samples. We successfully retrieved six near-­complete mitochondrial genomes from two sites within the aye-­aye’s geographic range that had not been sampled previously. Our method demonstrates the application of next-­ generation molecular techniques to species of conservation concern. This method can likely be applied to alternative foraged remains to sample endangered species other than aye-­ayes.

Transcriptome-based exon capture methods provide an approach to recover several hundred markers from genomic DNA, allowing for robust phylogenetic estimation at deep timescales. We applied this method to a highly diverse group of venomous marine snails, Conoidea, for which published phylogenetic trees remain mostly unresolved for the deeper nodes. We targeted 850 protein coding genes (678,322 bp) in ca. 120 samples, spanning all (except one) known families of Conoidea and a broad selection of non-Conoidea neogastropods. The capture was successful for most samples, although capture efficiency decreased when DNA libraries were of insufficient quality and/or quantity (dried samples or low starting DNA concentration) and when targeting the most divergent lineages. An average of 75.4% of proteins was recovered, and the resulting tree, reconstructed using both supermatrix (IQ-tree) and supertree (Astral-II, combined with the Weighted Statistical Binning method) approaches, are almost fully supported. A reconstructed fossil-calibrated tree dates the origin of Conoidea to the Lower Cretaceous. We provide descriptions for two new families. The phylogeny revealed in this study provides a robust framework to reinterpret changes in Conoidea anatomy through time. Finally, we used the phylogeny to test the impact of the venom gland and radular type on diversification rates. Our analyses revealed that repeated losses of the venom gland had no effect on diversification rates, while families with a breadth of radula types showed increases in diversification rates, thus suggesting that trophic ecology may have an impact on the evolution of Conoidea.

Ancient migrations in Southeast Asia The past movements and peopling of Southeast Asia have been poorly represented in ancient DNA studies (see the Perspective by Bellwood). Lipson et al. generated sequences from people inhabiting Southeast Asia from about 1700 to 4100 years ago. Screening of more than a hundred individuals from five sites yielded ancient DNA from 18 individuals. Comparisons with present-day populations suggest two waves of mixing between resident populations. The first mix was between local hunter-gatherers and incoming farmers associated with the Neolithic spreading from South China. A second event resulted in an additional pulse of genetic material from China to Southeast Asia associated with a Bronze Age migration. McColl et al. sequenced 26 ancient genomes from Southeast Asia and Japan spanning from the late Neolithic to the Iron Age. They found that present-day populations are the result of mixing among four ancient populations, including multiple waves of genetic material from more northern East Asian populations. Science , this issue p. 92 , p. 88 ; see also p. 31 , Ancient genomes reveal four layers of human migration into Southeast Asia. , The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.

We report two mitochondrial genomes of headstanders, derived from target capture and Illumina sequencing (HiSeq 2500 PE100). One trans-Andean species Megaleporinus muyscorum (mitochondrial consensus genome of 25 individuals) from Colombia and one cis-Andean species M. obtusidens from Argentina. Regarding M. muyscorum, mitochondrial genome has 13 protein-coding genes, 1 D-loop, 2 ribosomal RNAs, 21 transfer RNAs, and is 14,434 bp in length, for M. obtusidens mitochondrial genome has 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and is 15,546 bp in length.

We report four mitochondrial genomes of South American electric knifefishes, derived from target capture and Illumina sequencing (HiSeq 2500 PE100). Two trans-Andean species Eigenmannia humboldtii (mitochondrial consensus genome of 25 individuals) and Sternopygus aequilabiatus (mitochondrial consensus genome of 30 individuals) from Colombia and two cis-Andean species Eigenmannia limbata from Suriname and Sternopygus macrurus from Argentina. Regarding Eigenmannia humboldtii, Eigenmannia limbata, and Sternopygus macrurus mitochondrial genomes have 13 protein-coding genes, 1 D-loop, 2 ribosomal RNAs, 22 transfer RNAs, and are 13,394 bp, 10,921 bp, and 13,013 bp in length respectively, for Sternopygus aequilabiatus mitochondrial genomes have 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and is 14,270 bp in length.

Aim: The Indonesian island of Sulawesi is home to thousands of endemic terrestrial animal species. Phylogeographical studies of some of these taxa revealed concordant distribution patterns (areas of endemism; AoEs), suggestive of a shared evolutionary or ecological mechanism driving divergence among various terrestrial taxa. Generally, AoEs have been attributed to Pleistocene marine incursions, geological fault zones and Sulawesi’s history as an archipelago. We test, for the first time, the hypothesis that population divergences are associated with unsuitable climate spaces at the boundaries between these areas.

Historical museum specimens are invaluable for morphological and taxonomic research, but typically the DNA is degraded making traditional sequencing techniques difficult to impossible for many specimens. Recent advances in Next-Generation Sequencing, specifically target capture, makes use of short fragment sizes typical of degraded DNA, opening up the possibilities for gathering genomic data from museum specimens. This study uses museum specimens and recent target capture sequencing techniques to sequence both Ultra-Conserved Elements (UCE) and exonic regions for lineages that span the modern spiders, Araneomorphae, with a focus on Palpimanoidea. While many previous studies have used target capture techniques on dried museum specimens (for example, skins, pinned insects), this study includes specimens that were collected over the last two decades and stored in 70% ethanol at room temperature. Our findings support the utility of target capture methods for examining deep relationships within Araneomorphae: sequences from both UCE and exonic loci were important for resolving relationships; a monophyletic Palpimanoidea was recovered in many analyses and there was strong support for family and generic-level palpimanoid relationships. Ancestral character state reconstructions reveal that the highly modified carapace observed in mecysmaucheniids and archaeids has evolved independently.