Explore the vast range of titles available.

Environmental DNA (eDNA) analysis is a revolutionary tool for non‐invasive, cost‐effective, and highly sensitive monitoring of species distribution and abundance; however, there remain some uncertainties related to eDNA detection and quantification, as well as limitations in terms of its ecological interpretation. Although these may be elucidated by better understanding the characteristics and dynamics of eDNA, insight into such basic eDNA information has been limited in this decade, contrary to the advancements in eDNA applications targeting various taxa and environments. This review compiled previous findings regarding the characteristics and dynamics of macrobial eDNA and provides insights into how the basic knowledge of eDNA can contribute to the refinement and development of eDNA analysis for biomonitoring and stock assessment. A literature survey revealed that studies on the cellular and molecular state of eDNA were particularly lacking (18/728 papers from 2008 to 2020), resulting in a limited understanding regarding the process of eDNA transport and degradation. This review highlighted a number of studies targeting various types of eDNA beyond short mitochondrial DNA fragments (nuclear eDNA, longer eDNA fragments, and larger eDNA particles) to show how information on the state of eDNA improves the reliability of species detection and accuracy of abundance estimation, as well as provide more detailed information on individuals other than their presence and abundance. Linking the state of eDNA to its application will advance the analysis of eDNA and improve its application as a tool for monitoring biodiversity, ecosystem function, and fisheries resources. The manuscript reviews the knowledge about characteristics and dynamics of eDNA from macro‐organisms based on the studies from 2008 to 2020. We especially point out the importance of understanding the state of eDNA and show the potential of utilizing it for updating current eDNA analysis as a better tool of biomonitoring and stock assessment.

Abstract Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.

Background Austropotamobius torrentium is a freshwater crayfish species native to central and south-eastern Europe, with an intricate evolutionary history and the highest genetic diversity recorded in the northern-central Dinarides (NCD). Its populations are facing declines, both in number and size across its entire range. By extanding current knowledge on the genetic diversity of this species, we aim to assist conservation programmes. Multigene phylogenetic analyses were performed using different divergence time estimates based on mitochondrial and, for the first time, nuclear DNA markers on the largest data set analysed so far. In order to reassess taxonomic relationships within this species we applied several species delimitation methods and studied the meristic characters with the intention of finding features that would clearly separate stone crayfish belonging to different phylogroups. Results Our results confirmed the existence of high genetic diversity within A. torrentium, maintained in divergent phylogroups which have their own evolutionary dynamics. A new phylogroup in the Kordun region belonging to NCD has also been discovered. Due to the incongruence between implemented species delimitation approaches and the lack of any morphological characters conserved within lineages, we are of the opinion that phylogroups recovered on mitochondrial and nuclear DNA are cryptic subspecies and distinct evolutionary significant units. Conclusions Geographically and genetically isolated phylogroups represent the evolutionary legacy of A. torrentium and are highly relevant for conservation due to their evolutionary distinctiveness and restricted distribution.

Knowledge as to the taxonomic status of enigmatic bat species often is hindered by limited availability of specimens. This is particularly true for aerial-hawking bats that are difficult to catch. One such species, “Hypsugo” joffrei, was originally described in Nyctalus due to its long and slender wings, but subsequently transferred to Pipistrellus, and most recently to Hypsugo, on the basis of morphology. Analysis of newly available material, which more than doubles the known specimens of this taxon, demonstrates that it is morphologically and genetically distinct from all other bat genera. We accordingly describe it as belonging to a new, monotypic genus. We provide a detailed description of its external and craniodental traits, measurements, and assessment of genetic relationships, including barcode sequences to facilitate its rapid identification in future. The new genus belongs to a group that includes the recently described Cassistrellus, as well as Tylonycteris, and its closest relative, Philetor. We also describe the echolocation calls emitted by members of the taxon in different situations, which may facilitate finding them in previously unsampled locations. Based on the new data, the species occurs from Nepal to North Vietnam and China, which suggests that it could be more widespread than previously thought.

Genetic connectivity and historical population expansion are characteristics that have largely been studied and observed in several members of the Lutjanidae family throughout the Western South Atlantic, particularly in Brazilian waters. In this study, the population genetic structure of Lutjanus jocu was investigated using four genomic regions: two from mitochondrial DNA (Control Region and Cytochrome B) and two nuclear genes (Delta 6 desaturase—intron 8 and Ribosomal Protein S7—intron 1), in 144 specimens distributed in six locations on the Atlantic coast of Brazil. The results revealed high levels of genetic diversity for both mtDNA and nuDNA markers, and intense gene flow, indicating, consistent with other studies, that this species is represented by a single genetic stock along the Brazilian coast. This is likely due to the high dispersal capacity of L. jocu larvae, driven by the main equatorial currents, as well as biological and ecological factors, contributing to a genetically homogeneous population. Historical demographic analysis and neutrality tests suggest that the species experienced population expansion, possibly during the Pleistocene. Information regarding the genetic structure of populations is extremely important, especially for species of high economic and fishing importance, and can be very useful in guiding stock management and management measures.

Turtles (Testudines) form a monophyletic group with a highly distinctive body plan. The taxonomy and phylogeny of turtles are still under discussion, at least for some clades. Whereas in most previous studies, only a few species or genera were considered, we here use an extensive compilation of DNA sequences from nuclear and mitochondrial genes for more than two thirds of the total number of turtle species to infer a large phylogeny for this taxon. Our results enable us to discuss previous hypotheses on species phylogeny or taxonomy. We are thus able to discriminate between competing hypotheses and to suggest taxonomical modifications. Finally, we pinpoint the remaining ambiguities for this phylogeny and the species for which new sequences should be obtained to improve phylogenetic resolution.

Implementing efforts to understand biogeographic distribution patterns and taxonomic limits within animal groups is crucial for addressing several challenges of modern zoology. Although avian phylogeography has been extensively investigated within the Western Palearctic, several families, such as shrikes, still display unresolved or neglected biogeographic patterns both between and within species, thus requiring further investigations. The Woodchat Shrike (Lanius senator) is a long-distance migratory species that exhibits three morphologically well-recognizable subspecies, whose boundaries have never been phylogenetically investigated. Here, we aimed to define the phylogeographic structure of Lanius senator throughout its breeding range and assess the genetic coherence with respect to the phenotypically described subspecies. We assembled a collection of 34 samples mainly from breeding populations of each subspecies and analysed them using four mtDNA and two nuDNA markers. We did not find clear phylogenetic structure in nuclear Ornithine Decarboxylase (ODC) and Myoglobin intron 2 (MYO), but all the four mtDNA loci (i.e., ND2, COI, cytb and CR) highlighted two main haplogroups: one including both the nominate subspecies L. s. senator and L. s. badius and a second one consisting of L. s. niloticus (the easternmost part of its range). Surprisingly, individuals phenotypically assigned to L. s. niloticus from Israel were genetically assigned to the senator/badius haplogroup. Moreover, genetic distances between haplogroups showed intermediate values between inter-intraspecies diversity usually reported for Passerines. We estimated a divergence time at ca. 890 kya (554-1.259 kya HPD). Our findings showed a mismatch in subspecies assignment using morphology and genetic information and a marked differentiation between the eastern L. s. niloticus and all other L. senator populations sampled.

Background The Out of Africa hypothesis, OOAH, was challenged recently in an extended mtDNA analysis, PPA (Progressive Phylogenetic Analysis), that identified the African human populations as paraphyletic, a finding that contradicted the common OOAH understanding that Hss had originated in Africa and invaded Eurasia from there. The results were consistent with the molecular Out of Eurasia hypothesis, OOEH, and Eurasian palaeontology, a subject that has been largely disregarded in the discussion of OOAH. Results In the present study the mtDNA tree, a phylogeny based on maternal inheritance, was compared to the nuclear DNA tree of the paternally transmitted Y-chromosome haplotypes, Y-DNAs. The comparison showed full phylogenetic coherence between these two separate sets of data. The results were consistent with potentially four translocations of modern humans from Eurasia into Africa, the earliest taking place ≈ 250,000 years before present, YBP. The results were in accordance with the postulates behind OOEH at the same time as they lent no support to the OOAH. Conclusions The conformity between the mtDNA and Y-DNA phylogenies of Hss is consistent with the understanding that Eurasia was the donor and not the receiver in human evolution. The evolutionary problems related to OOAH became similarly exposed by the mtDNA introgression that took place from Hss into Neanderthals ≈ 500,000 YBP, a circumstance that demonstrated the early coexistence of the two lineages in Eurasia.

Background The molecular out of Africa hypothesis, OOAH, has been considered as an established fact amid population geneticists for some 25–30 years despite the early concern with it among phylogeneticists with experience beyond that of Homo . The palaeontological support for the hypothesis is also questionable, a circumstance that in the light of expanding Eurasian palaeontological knowledge has become accentuated through the last decades. Results The direction of evolution in the phylogenetic tree of modern humans ( Homo sapiens sapiens , Hss ) was established inter alia by applying progressive phylogenetic analysis to an mtDNA sampling that included a Eurasian, Lund, and the African Mbuti, San and Yoruba. The examination identified the African populations as paraphyletic, thereby compromising the OOAH. The finding, which was consistent with the out of Eurasia hypothesis, OOEH, was corroborated by the mtDNA introgression from Hss into Hsnn (Neanderthals) that demonstrated the temporal and physical Eurasian coexistence of the two lineages. The results are consistent with the palaeontologically established presence of H. erectus in Eurasia, a Eurasian divergence between H. sapiens and H. antecessor ≈ 850,000 YBP, an Hs divergence between Hss and Hsn (Neanderthals + Denisovans) ≈ 800,000 YBP, an mtDNA introgression from Hss into Hsnn*  ≈ 500,000 YBP and an Eurasian divergence among the ancestors of extant Hss ≈ 250,000 YBP at the exodus of Mbuti/San into Africa. Conclusions The present study showed that Eurasia was not the receiver but the donor in Hss evolution. The findings that Homo left Africa as erectus and returned as sapiens sapiens constitute a change in the understanding of Hs evolution to one that conforms to the extensive Eurasian record of Hs palaeontology and archaeology.

The stink bug, Megacopta cribraria, has an obligate relationship with a bacterial endosymbiont which allows it to feed on legumes. The insect is a pest of soybeans in Asia and was first reported in the Western Hemisphere in October 2009 on kudzu vine, Pueraria montana, in North Georgia, USA. By October 2010 M. cribraria had been confirmed in 80 counties in Georgia actively feeding on kudzu vine and soybean plants. Since the symbiosis may support the bug’s ecological expansions, a population genetic baseline for the symbiosis was developed from mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) gene sequence collected from each insect and its primary g- proteobacterium and secondary a -proteobacterium endosymbionts. A single mitochondrial DNA haplotype was found in all insects sampled in Georgia and South Carolina identified as GA1. The GAI haplotype appears to be rapidly dispersing across Georgia and into contiguous states. Primary and secondary endosymbiont gene sequences from M. cribraria in Georgia were the same as those found in recently collected Megacopta samples from Japan. The implications of these data are discussed.