<p>U&nbsp; ovom&nbsp; radu&nbsp; sagledan&nbsp; je&nbsp; molekularni&nbsp; diverzitet,&nbsp; filogeografska&nbsp; struktura,<br />prostorna&nbsp; distribucija&nbsp; molekularnog&nbsp; diverziteta,&nbsp; kao&nbsp; i&nbsp; prisustvo&nbsp; selekcionih<br />signala i genetičkih signala lokalnih adaptacija kod 251 jedinke&nbsp; vrste&nbsp; Lepus<br />europaeus (Pallas,&nbsp; 1778)&nbsp; sa&nbsp; teritorije&nbsp; Evrope&nbsp; i&nbsp; Bliskog&nbsp; Istoka,&nbsp; a&nbsp; na&nbsp; osnovu<br />analize&nbsp; varijabilnosti&nbsp; sekvenci&nbsp; D&nbsp; petlje&nbsp; mtDNK, MT-ND2,&nbsp; MT-ND6,&nbsp; MHCDQA, MHC-DQB i TLR2 gena. Uočen je visok nivo parametara molekularnog<br />diverziteta&nbsp; za&nbsp; sve&nbsp; ispitivane&nbsp; molekularne&nbsp; markere.&nbsp; Utvrđeno&nbsp; je&nbsp; postojanje<br />filogeografske&nbsp; strukturiranosti&nbsp; vrste&nbsp; na&nbsp; osnovu&nbsp; mtDNK,&nbsp; kao&nbsp; i&nbsp; asimetričan<br />protok gena jedinki sa teritorije Anadolije na teritoriju Balkana&nbsp; na osnovu D<br />petlje mtDNK, MT-ND2 i MT-ND6 gena, dok je na osnovu sekvenci D petlje<br />mtDNK uočena gotovo tri puta veća stopa protoka gena sa Balkana u centralnu<br />i&nbsp; zapadnu&nbsp; Evropu.&nbsp; Utvrđeno&nbsp; je&nbsp; prisustvo&nbsp; signala&nbsp; poizivne&nbsp; selekcije&nbsp; u&nbsp; okviru<br />MT-ND6&nbsp; gena,&nbsp; kao&nbsp; i&nbsp; efekat&nbsp; klimatskih&nbsp; parametara&nbsp; (precipitacije)&nbsp; na<br />distribuciju&nbsp; proteinskih&nbsp; varijanti&nbsp; ND6C&nbsp; i&nbsp; ND6F,&nbsp; kao&nbsp; moguća&nbsp; posledica<br />regionalnih adaptacija na razlike u sredinskim uslovima. Pokazano je odsustvo<br />signala&nbsp; filogeografske&nbsp; strukturiranosti&nbsp; na&nbsp; osnovu MHC-DQA, MHC-DQB i<br />TLR2 gena.&nbsp; Uočeno&nbsp; je&nbsp; postojanje&nbsp; prostorne&nbsp; strukturiranosti&nbsp; na&nbsp; osnovu&nbsp; gena<br />imunskog&nbsp; sistema,&nbsp; i&nbsp; definisane&nbsp; su&nbsp; dve&nbsp; prostorne&nbsp; grupe,&nbsp; jedna&nbsp; koja&nbsp; je<br />obuhvatala&nbsp; jedinke&nbsp; sa&nbsp; teritorije&nbsp; Bliskog&nbsp; Istoka,&nbsp; i&nbsp; druga&nbsp; koja&nbsp; je&nbsp; obuhvatala<br />jedinke&nbsp; sa&nbsp; teritorije&nbsp; Evropi.&nbsp; Vi&scaron;e&nbsp; vrednosti&nbsp; parametara&nbsp; molekularnog<br />diverziteta uočene su u anadolijskoj grupi, u poređenju sa evropskom grupom.<br />Uočen je signal delovanja pozitivne i negativne selekcije u MHC-DQA i MHCDQB genima, kao i signal negativne selekcije u TLR2 genu. Pokazan je efekat<br />klimatskih&nbsp; parametara&nbsp; na&nbsp; distribuciju&nbsp; najzastupljenijih&nbsp; proteinskih&nbsp; varijanti<br />MHC-DQA&nbsp; i&nbsp; MHC-DQB&nbsp; gena kao&nbsp; indirektni&nbsp; pokazatelj&nbsp; imunogenetičkih<br />adaptacija&nbsp; na&nbsp; sredinski&nbsp; uslovljene&nbsp; pretpostavljene&nbsp; razlike&nbsp; u&nbsp; distribuciji<br />patogena.&nbsp; Mehanizam&nbsp; oblikovanja&nbsp; varijabilnosti&nbsp; MHC&nbsp; gena&nbsp; rezultat&nbsp; je<br />uzajamnog delovanja mutacija, rekombinacija i selekcije.</p> / <p>In&nbsp; this&nbsp; doctoral&nbsp; dissertation,&nbsp; molecular&nbsp; diversity,&nbsp; phylogeographic&nbsp; structure,<br />spatial&nbsp; distribution&nbsp; of&nbsp; molecular&nbsp; diversity,&nbsp; detection&nbsp; of&nbsp; possible&nbsp; selection<br />signals&nbsp; shaping&nbsp; the&nbsp; evolution of&nbsp; these&nbsp; genes,&nbsp; as&nbsp; well&nbsp; as&nbsp; the&nbsp; presence&nbsp; of<br />local/regional&nbsp; adaptations&nbsp; in&nbsp; correlation&nbsp; was&nbsp; examined&nbsp; in&nbsp; 251&nbsp; brown&nbsp; hares<br />from&nbsp; Europe&nbsp; and&nbsp; the&nbsp; Middle East&nbsp; based&nbsp; on&nbsp; the&nbsp; analyses&nbsp; of&nbsp; mitochondrial&nbsp; D<br />loop,&nbsp; mitochondrially&nbsp; Encoded&nbsp; NADH&nbsp; Dehydrogenase&nbsp; 2&nbsp; (MT-ND2),<br />mitochondrially&nbsp; Encoded&nbsp; NADH&nbsp; Dehydrogenase&nbsp; 6&nbsp; (MT-ND6),&nbsp; exon&nbsp; 2&nbsp; of<br />MHC Class II genes MHC-DQA,MHC-DQB and Toll Like Receptor 2 (TLR2)<br />gene sequences. A high level of molecular diversity was found based on the all<br />applied&nbsp; markers.&nbsp; Strong&nbsp; signal&nbsp; of&nbsp; phylogeographical&nbsp; and&nbsp; spatial&nbsp; structuring<br />was&nbsp; observed&nbsp; for&nbsp; mtDNA,&nbsp; most&nbsp; likely&nbsp; as&nbsp; a&nbsp; consequence&nbsp; of&nbsp; climatic<br />perturbations&nbsp; during&nbsp; the&nbsp; Pleistocene.&nbsp; The&nbsp; evolutionary&nbsp; development&nbsp; of&nbsp; hares<br />from&nbsp; Anatolia/Israel&nbsp; to&nbsp; the&nbsp; Balkans,&nbsp; and&nbsp; furthermore&nbsp; to&nbsp; central&nbsp; and&nbsp; western<br />Europe was suggested by several lines of evidences, which include dating the<br />population&nbsp; demography&nbsp; based&nbsp; on&nbsp; D-loop&nbsp; sequences,&nbsp; the&nbsp; observed&nbsp; migration<br />patterns,&nbsp; results&nbsp; of&nbsp; demographic&nbsp; tests,&nbsp; and&nbsp; apparent&nbsp; reduction&nbsp; in&nbsp; molecular<br />diversity&nbsp; indices&nbsp; along&nbsp; this&nbsp; trajectory.&nbsp; Positive&nbsp; selection&nbsp; acting&nbsp; on MT-ND6<br />gene&nbsp; was&nbsp; detected,&nbsp; together&nbsp; with&nbsp; significant&nbsp; climatic&nbsp; effect&nbsp; shaping&nbsp; the<br />distribution&nbsp; of&nbsp; the&nbsp; most&nbsp; prevalent&nbsp; protein&nbsp; variants&nbsp; found&nbsp; in&nbsp; this&nbsp; gene,<br />supposedly&nbsp; as&nbsp; a&nbsp; consequence&nbsp; to&nbsp; local/regional&nbsp; adaptations&nbsp; due&nbsp; to&nbsp; the<br />environmentally induced different energetic requirements and optimization of<br />OXPHOS&nbsp; genes.&nbsp; On&nbsp; the&nbsp; other&nbsp; side,&nbsp; less&nbsp; evident&nbsp; phylogeographic&nbsp; signal&nbsp; and<br />absence&nbsp; of&nbsp; strong&nbsp; structuring&nbsp; was&nbsp; revealed&nbsp; in&nbsp; MHC&nbsp; genes.&nbsp; High&nbsp; diversity&nbsp; at<br />MHC genes seems to be shaped by the interplay of recombination, selection<br />mechanisms&nbsp; and&nbsp; adaptations.&nbsp; Balancing&nbsp; selection&nbsp; seems&nbsp; to&nbsp; maintain&nbsp; a&nbsp; high<br />molecular&nbsp; diversity&nbsp; within&nbsp; these&nbsp; genes,&nbsp; while&nbsp; directional selection&nbsp; promotes<br />local/regional adaptations to pathogenic landscapes, as indirectly suggested by<br />a&nbsp; significant&nbsp; effect&nbsp; of&nbsp; climatic&nbsp; parameters&nbsp; on&nbsp; the&nbsp; distribution&nbsp; of&nbsp; protein<br />variants in both examined MHC genes.</p>

I used mitochondrial COI sequence data from forty one individuals to investigate phylogenetic relationships among populations of two morphologically similar species of the pseudoscorpion genus Apochthonius, A. minimus and A. occidentalis, in western Washington, Oregon, and northern California. My goal was to assess whether genetic structure in the two species was congruent with geography. Many plant and animal species in the Pacific Northwestern United States have shown patterns of genetic differentiation that follow both north-south and east-west trends, indicating that geologic and climatic events in the past separated populations to the extent that they became genetically differentiated. A distinct geographic pattern emerged within A. occidentalis, with at least one northern and two southern populations. A clade containing all A. minimus sequences was recovered. However, this clade falls within the larger clade of A. occidentalis, rendering A. occidentalis paraphyletic. Furthermore, the A. minimus sequences showed north-south geographic structuring within the clade. Population genetic analyses were performed based on geographic location within the Pacific Northwest. I found high genetic differentiation coupled with low gene flow between most populations, with the exception of the Portland and North Coast Range populations. These data suggest the presence of more than two species of Apochthonius in the Pacific Northwest.

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Population structure, biogeography and phylogenetic relationships of the fruit bat genus Rousettus have been studied in Africa and adjacent regions. The current population patterns of rousettine fruit bats in the Old World are influenced by several environmental attributes, namely the topography, climate and land cover. These variables are mirrored in fruit bat plesiomorphies related to the ecological niche of tropical flying frugivore, as well as apomorphies of rousettines including echolocation ability, roosting in caves and dispersal capacity in open landscapes with discontinuous tree cover. Phylogenetic relationships among species and subspecies of the genus have been indicated and confronted with the existing colonization scenarios. Insular populations (including habitat islands within desert oases) show frequent genetic differentiation from their mainland relatives suggesting successful founder events after traversing stretches of unsuitable habitats. Genetic differentiation evolving in less distant islands suggests involving behavioural mechanisms maintaining cohesion of isolated demes as site fidelity and natal habitat-biased dispersal. In sub-Saharan mainland Africa within the large range reaching from the southern border of Sahara to Cape Peninsula, Rousettus populations share a...

The mountain whitefish (Prosopium williamsoni) has been largely overlooked in population genetic analyses despite its wide distribution in discrete drainage basins in western North America for over four million years. Its closest sister taxa the Bear Lake whitefish (P. abyssicola), Bonneville cisco (P. gemmifer), and Bonneville whitefish (P. spilonotus) are found only in Bear Lake Idaho-Utah and were also included in the analyses. A total of 1,334 cytochrome b and 1,371 NADH dehydrogenase subunit 2 sequences from the Bonneville Basin, the Columbia River Sub-basin, the lower Snake River Sub-basin, the upper Snake River Sub-basin, the Green River Basin, the Lahontan Basin, and the Missouri Basin were examined to test for geographically based genetic differentiation between drainage basins and sub-basins and phylogeographic relationships to determine the invasion route of Prosopium into western North America and to aid in understanding current relationships. Prosopium entered the region via the Missouri River connection to Hudson Bay and moved in two waves: one colonized the lower Snake River Sub-basin, Columbia River Sub-basin, and the Lahontan Basin; the second wave colonized the upper Snake River Sub-basin, Bonneville Basin, Green River Basin, and established the Bear Lake Prosopium. Mountain whitefish exhibit a large amount of geographical genetic differentiation based on drainage basin except between the upper Snake River and the Bonneville Basin while the Bear Lake Prosopium show large amounts of gene flow between the three species. The apparent paraphyly of the mountain whitefish and the limited genetic structure of the Bear Lake Prosopium warrant recognition in the management of Prosopium and raise questions regarding species definitions in the group.

Phylogeography and molecular phylogenetics have proven remarkably useful for understanding the patterns and processes influencing historical diversification of biotic lineages at and below the species level, as well as delimiting morphologically cryptic species. In this dissertation, I used an integrative approach coupling comparative phylogeography and coalescent-based species delimitation to improve our understanding of the biogeography and species limits of Central American freshwater fishes. In Chapter 1, I conducted a literature review of the contributions of phylogeography to understanding the origins and maintenance of lower Central American biodiversity, in light of the geological and ecological setting. I highlighted emerging phylogeographic patterns, along with the need for improving regional historical biogeographical inference and conservation efforts through statistical and comparative phylogeographic studies. In Chapter 2, I compared mitochondrial phylogeographic patterns among three species of livebearing fishes (Poeciliidae) codistributed in the lower Nicaraguan depression and proximate uplands. I found evidence for mixed spatial and temporal divergences, indicating phylogeographic “pseudocongruence” suggesting that multiple evolutionary responses to historical processes have shaped population structuring of regional freshwater biota, possibly linked to recent community assembly and/or the effects of ecological differences among species on their responses to late Cenozoic environmental events. In Chapter 3, I used coalescent-based species tree and species delimitation analyses of a multilocus dataset to delimit species and infer their evolutionary relationships in the Poecilia sphenops species complex (Poeciliidae), a widespread but morphologically conserved group of fishes. Results indicated that diversity is underestimated and overestimated in different clades by c. ±15% (including candidate species); that lineages diversified since the Miocene; and that some evidence exists for a more probable role of hybridization, rather than incomplete lineage sorting, in shaping observed gene tree discordances. Last, in Chapter 4, I used a comparative phylogeographical analysis of eight codistributed species/genera of freshwater fishes to test for shared evolutionary responses predicted by four drainage-based hypotheses of Neotropical fish diversification. Integrating phylogeographic analyses with paleodistribution modeling revealed incongruent genetic structuring among lineages despite overlapping ancestral Pleistocene distributions, suggesting multiple routes to community assembly. Hypotheses tests using the latest approximate Bayesian computation model averaging methods also supported one pulse of diversification in two lineages diverged in the San Carlos River, but multiple divergences of three lineages across the Sixaola River basin, Costa Rica, correlated to Neogene sea level events and continental shelf width. Results supported complex biogeographical patterns illustrating how species responses to historical drainage-controlling processes have influenced Neotropical fish diversification.

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