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Conservation biologists often deal with species that have small, fragmented populations throughout their range, making it necessary to prioritize populations for management. Genetics provides tools to assist with prioritization according to the levels and distribution of genetic diversity and evolutionary distinctiveness. Many studies have used nuclear microsatellite loci to measure genetic diversity in disparate populations and mitochondrial DNA to assess genetic distinctiveness. However, comparing metrics based on microsatellite genotypes ascertained in different laboratories is complicated by the selection of different loci with distinct nucleotide repeat motifs. This issue may be resolved by comparing metrics to a well-characterized reference population with shared microsatellite markers. The Asian elephant, Elephas maximus, is an endangered species with 50–60% of populations in India and Sri Lanka, and small, fragmented populations throughout southeast and insular Asia. We assessed range-wide genetic diversity of the Asian elephant by directly comparing allelic diversity and heterozygosity estimates from 35 populations, overcoming marker selection bias by calibrating metrics to a large population on the Nakai Plateau, Lao PDR, genotyped at 25 loci. We coupled these results with mtDNA analysis to evaluate genetic distinctiveness and identify potential conservation management units. We found the greatest diversity in the populations of southeast Asia and the greatest genetic distinctiveness among the subspecies designations, particularly Borneo and Sumatra, and other southeast Asian populations. The populations of southeast Asia, albeit small, fragmented, and at high risk of extirpation, contain valuable diversity and distinctiveness and are thus of high priority for the preservation of the Asian elephant. [ABSTRACT FROM AUTHOR]

Glacial cycles and pre-glacial drainage patterns have imbued the Interior Highlands of the United States with a rich suite of freshwater taxa and phylogroups. However, supplementation of sportfish from the Great Lakes into the waterbodies of this region, including the Missouri, Ouachita, Black, White, and Little Red River drainages, may have obscured phylogeographic patterns. Walleye (Sander vitreus), one of the most common sportfish in the eastern US, inhabit the Interior Highlands but their population genetic composition and structure in this region has received little attention. We examined the genetic composition of walleye (n = 643) in the Interior Highlands using microsatellite markers and a subsample (n = 188) with mitochondrial DNA and found significant genetic differences among walleye in our study area. Walleye from the Missouri, Ouachita, White, and Little Red drainages were most closely related to a Great Lakes reference sample, a common stocking source. However, the Black River, in the easternmost portion of the Interior Highlands, contained walleye with mitochondrial DNA that was closely related to walleye from the Eastern Highlands. The remainder of the study area drainages contained a mix of walleye groups, more closely related to Great Lakes rather than Highlands walleye but not definitively the product of stocking. Though managers have relied on mitochondrial markers for stock identification in the past, we recommend that walleye in regions receiving little research attention be analyzed with nuclear markers to better understand and preserve genetic diversity and that managers stock with local walleye only within the drainages that we identified as genetically distinct: Black, Missouri, and White/Little Red/Ouachita. [ABSTRACT FROM AUTHOR]

The Lake Sturgeon Acipenser fulvescens is native to three major watersheds in the USA: the Great Lakes, Hudson Bay, and Mississippi River drainages. However, they have declined across much of their range due to overfishing, pollution, and major river alterations. After their near extirpation in Missouri, the Missouri Department of Conservation initiated a reintroduction program to restore the Lake Sturgeon in the state's largest waterways. From 1984 to 2015, offspring originating from Lake Winnebago (1984–2001) and from upper Mississippi River tributaries (2004–2015) were reared in captivity and released into portions of the Mississippi and Missouri rivers. After 32 years of restorative releases, we screened Lake Sturgeon samples from the state of Missouri by using 11 microsatellite loci and mitochondrial DNA control region sequences. We examined overall genetic diversity and genetic structure of Lake Sturgeon captured in the Mississippi and Missouri rivers for differences between rivers and among groups within rivers. We found high levels of genetic diversity within both rivers, with very little genetic differentiation between them. Higher‐than‐average relatedness within sample groups and heterozygote excess were consistent with the pattern expected from stocked fish and suggested that closely related fish may have aggregated at stocking sites. We detected two genetic groups in Missouri, reflecting the change in stock source. Haplotypes that may be unique to the Mississippi and Ohio River systems were observed at very low frequencies. Though largely the product of stocking, reproductively mature Lake Sturgeon will likely have sufficient genetic diversity and will have experienced selection pressures in Missouri's large rivers, making them the most appropriate source for further supplementation if it is deemed necessary. We recommend continued research and monitoring of reproductive habits and preservation of multiple spawning sites to continue the long path toward a self‐sustaining Lake Sturgeon population in Missouri's waters. [ABSTRACT FROM AUTHOR]

The white‐tailed deer (Odocoileus virginianus) of Missouri have undergone changes in the past 100 years. From a historical estimate of 700,000 individuals, deer were nearly extirpated from the state following overexploitation in the late 1800s. Despite this, deer have since undergone a rapid expansion to the current population of 1.4 million. Because of this complex recent history, we sought to understand the levels and distribution of genetic diversity in deer across Missouri. We genotyped 751 deer at 10 microsatellite loci and used genetic distance metrics and Bayesian clustering analyses to identify distinct genetic groups. We also sequenced the mitochondrial control region from a subset (n = 248) of deer to identify historical lineages. We found high levels of nuclear marker diversity (HE = 0.818) and low, but statistically significant, levels of differentiation among regions. The high level of mitochondrial diversity (48 haplotypes; haplotype diversity = 0.621–0.964) is reflected in a haplotype network that suggests the persistent signature of translocated lineages. Overall, the white‐tailed deer of Missouri now represent a highly diverse population with no indication that there are barriers to gene flow. This will be an important consideration for the management of disease resistance and spread throughout the state. © 2018 The Wildlife Society. White‐tailed deer were nearly extirpated from Missouri following overexploitation in the late 1800s but have since undergone a rapid expansion to the current population of 1.4 million. We report high levels of genetic diversity and low levels of differentiation across the state, which will be an important consideration for the management of disease resistance and spread. [ABSTRACT FROM AUTHOR]

As species evolve, they become adapted to their local environments. Detecting the genetic signature of selection and connecting that to the phenotype of the organism, however, is challenging. Here we report using an integrative approach that combines DNA sequencing with structural biology analyses to assess the effect of selection on residues in the mitochondrial DNA of the two species of African elephants. We detected evidence of positive selection acting on residues in complexes I and V, and we used homology protein structure modeling to assess the effect of the biochemical properties of the selected residues on the enzyme structure. Given the role these enzymes play in oxidative phosphorylation, we propose that the selected residues may contribute to the metabolic adaptation of forest and savanna elephants to their unique habitats. [ABSTRACT FROM AUTHOR]

We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana) in East Africa, using microsatellite and mitochondrial DNA (mtDNA) markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p,0.05) as measured with both mtDNA haplotypes and microsatellites. Only the samples from the adjacent Maasai Mara and Serengeti ecosystems showed no significant differentiation. A phylogenetic neighbour-joining tree constructed from mtDNA haplotypes detected four clades. Clade four corresponds to the F clade of previous mtDNA studies that reported to have originated in forest elephants (Loxodonta cyclotis) but to also be present in some savannah elephant populations. The split between clade four and the other three clades corresponded strongly to the geographic distribution of mtDNA haplotypes across the rift valley in the study area. Clade four was the dominant clade detected on the west side of the rift valley with rare occurrences on the east side. Finally, the strong patterns of population differentiation clearly indicated that the recent colonists to the community-owned land in Kenya came from the west side of the rift valley. Our results indicate strong female philopatry within the isolated populations of the trans rift valley region, with gene flow primarily mediated via male movements. The recent colonization event from Maasai Mara or Serengeti suggests there is hope for maintaining connectivity and population viability outside formal protected areas in the region. [ABSTRACT FROM AUTHOR]

Previous studies have examined germ-line mutations to infer the processes that generate and maintain variability in microsatellite loci. Few studies, however, have examined patterns to infer processes that act: on microsatellite loci over evolutionary time. Here, we examine changes in 8 dipucleotide loci across the adaptive radiation of Hawaiian honeycreepers. The loci were found to be highly variable across the radiation, and we did not detect ascertainment bias with respect to allelic diversity or allele size ranges. in examining patterns at the sequence level, we found that changes in flanking regions, repeat motifs, or repeat interruptions were often shared between closely related species and may be phylogenetically informative. Genetic distance measures based on microsatellites were strongly correlated with those based on mitochondrial DNA (mtDNA) sequences as well as with divergence time up to 3 My. Phylogenetic inferences based on microsatellite genetic distances consistently recovered 2 of the 4 honeycreeper clades observed in a tree based on mtDNA sequences but differed from the mtDNA tree in the relationships among clades. Our results confirm that microsatellite loci may be conserved over evolutionary time, making them useful in population-level studies of species that diverged from the species in which they were characterized as long as 5 Ma. Despite this, we found that their use in phylogenetic inference was limited to closely related honeycreeper species. [ABSTRACT FROM AUTHOR]

The elephants of the Knysna region continue to survive, despite fears that there was only a single surviving female. Their range is larger than previously believed, and includes the Afromontane forest and mountain fynbos. The five individuals detected in this study were all females, and share a single mitochondrial DNA control region haplotype with individuals from Addo Elephant National Park. At least two of these elephants appear to be first-order relatives, and the others may be part of a single matrilineal group. The genetic diversity detected is lower than that found in most African savanna populations, but is higher than that found at Addo, where individuals represent the descendents of a severe population size bottleneck. Levels of genetic diversity are more similar to those detected at Kruger National Park, suggesting that the Knysna elephants represent a remnant of the once widespread populations of South Africa. [ABSTRACT FROM AUTHOR]

The loggerhead shrike ( Lanius ludovicianus), a songbird that hunts like a small raptor, maintains breeding populations on seven of the eight California Channel Islands. One of the two subspecies, L. l. anthonyi, was described as having breeding populations on six of the islands while a second subspecies, L. l. mearnsi, was described as being endemic to San Clemente Island. Previous genetic studies have demonstrated that the San Clemente Island loggerhead shrike is well differentiated genetically from both L. l. anthonyi and mainland populations, despite the fact that birds from outside the population are regular visitors to the island. Those studies, however, did not include a comparison between San Clemente Island shrikes and the breeding population on Santa Catalina Island, the closest island to San Clemente. Here we use mitochondrial control region sequences and nuclear microsatellites to investigate the population structure of loggerhead shrikes in the Channel Islands. We confirm the genetic distinctiveness of the San Clemente Island loggerhead shrike and, using Bayesian clustering analysis, demonstrate the presence and infer the source of the nonbreeding visitors. Our results indicate that Channel Island loggerhead shrikes comprise three distinct genetic clusters that inhabit: (i) San Clemente Island, (ii) Santa Catalina Island and (iii) the Northern Channel Islands and nearby mainland; they do not support a recent suggestion that all Channel Island loggerhead shrikes should be managed as a single entity. [ABSTRACT FROM AUTHOR]

Extensive phylogenetic studies have found robust phylogenies are modeled by using a multi-gene approach and sampling from the majority of the taxa of interest. Yet, molecular studies focused on the lorises, a cryptic primate family, have often relied on one gene, or just mitochondrial DNA, and many were unable to include all four genera in the analyses, resulting in inconclusive phylogenies. Past phylogenetic loris studies resulted in lorises being monophyletic, paraphyletic, or an unresolvable trichotomy with the closely related galagos. The purpose of our study is to improve our understanding of loris phylogeny and evolutionary history by using a multi-gene approach. We used the mitochondrial genes cytochrome b , and cytochrome c oxidase subunit 1, along with a nuclear intron (recombination activating gene 2) and nuclear exon (the melanocortin 1 receptor). Maximum Likelihood and Bayesian phylogenetic analyses were conducted based on data from each locus, as well as on the concatenated sequences. The robust, concatenated results found lorises to be a monophyletic family (Lorisidae) (PP ≥ 0.99) with two distinct subfamilies: the African Perodictinae (PP ≥ 0.99) and the Asian Lorisinae (PP ≥ 0.99). Additionally, from these analyses all four genera were all recovered as monophyletic (PP ≥ 0.99). Some of our single-gene analyses recovered monophyly, but many had discordances, with some showing paraphyly or a deep-trichotomy. Bayesian partitioned analyses inferred the most recent common ancestors of lorises emerged ∼42 ± 6 million years ago (mya), the Asian Lorisinae separated ∼30 ± 9 mya, and Perodictinae arose ∼26 ± 10 mya. These times fit well with known historical tectonic shifts of the area, as well as with the sparse loris fossil record. Additionally, our results agree with previous multi-gene studies on Lorisidae which found lorises to be monophyletic and arising ∼40 mya ( Perelman et al., 2011; Pozzi et al., 2014 ). By taking a multi-gene approach, we were able to recover a well-supported, monophyletic loris phylogeny and inferred the evolutionary history of this cryptic family. [ABSTRACT FROM AUTHOR]

Baylisascaris procyonis is a nematode of significant concern to public and domestic animal health as well as wildlife management. The population genetics of B. procyonis is poorly understood. To gain insights into patterns of genetic diversity within (infrapopulation level) and among (component population level) raccoon ( Procyon lotor ) hosts, and specifically to assess the relative importance of indirect and direct transmission of the parasite for explaining observed population structure, we collected 69 B. procyonis from 17 wild raccoons inhabiting five counties in Missouri and Arkansas, USA. Informative regions of mitochondrial (CO1, CO2) and nuclear (28S, ITS2) genes were amplified and the distribution and genetic variability of these genes were assessed within and across raccoons. Concatenation of the CO1 and CO2 mtDNA sequences resulted in 5 unique haplotypes, with haplotype diversity 0.456 ± 0.068. The most common haplotype occurred in 94% of raccoons and 72.5% of B. procyonis. Sequences for 28S rDNA revealed four unique nuclear genotypes, the most common found in 100% of raccoons and 82.6% of B. procyonis . ITS2 genotypes were assessed using fragment analysis, and there was a 1:1 correspondence between 28S and ITS-2 genotypes. Infrapopulation variation in haplotypes and genotypes was high and virtually all hosts infected with multiple sequenced nematodes also harbored multiple haplotypes and genotypes. There was a positive relationship between the size of the analyzed infrapopulation (i.e., the number of nematodes analyzed) and the number of haplotypes identified in an individual. Collectively this work emphasizes the importance of indirect transmission in the lifecycle to this parasite. [ABSTRACT FROM AUTHOR]